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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

Basic information

species Zea mays
transcript GRMZM2G181151_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 13
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
||| | | |  || |||||   |  ||||||       | |||    |  ||||      | || |   |||      ||  | |  | ||||||||  | || ||||||||||||||||| |||||||| |||||||| ||||||||||| || || || ||||||||||| ||||| ||||||||||||
gtaaacatttggactccat---acatttgat-------ttcat---ttaagctatggcaaatacttacagtg------gagctcatttatgctgtttcatgttacagCTTTATGCCAACTATGCAATTGGGAAGGATGTCCAGGCCATGAAAGCCGTTGTGGGAGAGGAGGCGCTCTCTTCTGAGGATCTG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 14
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagac-atgatgtgcaagatga-attgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
                       | | |||| | |   |    | ||   | ||   ||| |   || |     |  ||   ||| |  | |  | || | | |||||||| ||||| || || || |||||||||||||| ||||| ||||| ||||| |||||||| || ||||| || |||||||| |||
----------------------gtctctgatcatgttttgttca-tcacagttatttttctgtttatcacacagactatctcattcatgt-tatttttatttttttcagCTCTATGCAAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA10G42940.3 (Glycine max), 3'ss of exon 13
gtacatactatgagtccatgttatttttgataagggagtccatagtc--tttgctacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
             |||  || | || ||  |     |   ||||||   ||| ||   | ||| | |   | |         ||| |  | |  | || | | |||||||| || || || || || || ||||||||||| ||||| ||||| ||||| |||||||| || ||||| || |||||||| |||
-------------gtctctgatcttgtt--ttgttcatcacatagttatttttctgttcatcacatagactatat----ctcattcatgt-tatttttatttttttcagCTCTACGCAAATTATGCTATCGGAAAGGATGTGCAGGCAATGAAAGCAGTGGTTGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 13
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
                     |  ||||| |     | | ||| |   ||  | |  || | |    || |         ||||     || | | ||   |||||||| ||||| || || || |||||||||||||| ||||| ||||| || || || ||||| || ||||| || |||||||| |||
------------------gtctggttttgcttgtttactacattgctattttttctgtttataagccatctt--------attgg----tgttttgtttcttttcagCTCTATGCAAATTATGCCATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 14
----gtacatactatgagtccat-gttatttttgataagggagtccata---gtctttgctacccttcagacatgat-gtgcaagatgaa-ttgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
    |    || |    ||||||    |   |||   |     |   |    ||   |  |||   |||    |  | |    || | || |||  ||    | |||    |||||| | |||||||| ||||| ||||||||||| || ||||||||||| || || |||||||| || || || || || |||||||||
gtaagactttatttcttgtccattaccagcattgcagaaaagctttgtttatgtaagttttacttgtcaacttttttagcctgagcttaacttgttattatgtttttgtgatttcagTTGTATGCCAATTACGCTATTGGAAAGGACGTGCAGGCCATGAAAGCCGTGGTTGGAGAAGAAGCTCTTTCTTCCGAGGATCTG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagacatgatgtgcaagatgaattgacatctgctg--ttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
          | ||     |     ||    ||| | ||   || | ||  | |   |   |   | | |         ||  |||  ||| ||  ||||| | ||||||| ||||| || || || |||||||||||||| ||||| ||||| || || || |||||||| |||||||| ||||||||||||
---------gtaagattcagaaggctt----aagtgtgtttttaattttctccattatattgctttaaggcctc---ctaaccgac-cctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 13
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
                   ||  | ||||||    | |    |    |   || | |||    || |            || |   ||  | |  ||  |||||||||| ||||| || || |||||||| ||||||||||| || ||||| || || |||||||| || ||||| || ||||||||||||
-------------------gtagtatttgatgttcgggc---tgcgttcaccttctctttgagcacgtccc--------aacta--atgcgattcttcttctttcagCTCTATGCAAATTATGCAATTGGGAAGGATGTTCAAGCAATGAAAGCTGTGGTTGGAGAAGAAGCACTTTCTTCTGAGGATCTG

upper sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 13
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctaccct-tcagacatg-atgtgcaagatgaat-tgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
 |   |  |   ||  ||||  | || | |      ||| | || |   |  |||    ||||  ||| ||  | ||  |  |  | |||||     ||  || |  ||| | ||||| || || || ||||||||||||||||| || |||||||| |||||||||||||| ||  | || || || ||||||
-tttttgtttcaag--catgcaacttctca------agtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatc-atgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60355003|gb|DN221976.1|DN221976
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|16925493|gb|BM078561.1|BM078561
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|4646659|gb|AI491497.2|AI491497
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|32945219|gb|CF050038.1|CF050038
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|211017023|gb|FL053488.1|FL053488
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|60343435|gb|DN210408.1|DN210408
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|211222466|gb|FL437622.1|FL437622
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATT-GAAAGGGATGTTCAGGCCATGAAGGCAGT
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAA-GGATGTTCAGGCCATGAAGGCAGT
EST: gi|60352479|gb|DN219452.1|DN219452
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|31664289|gb|CD573014.1|CD573014
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|211122809|gb|FL454319.1|FL454319
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|67019767|gb|CO448516.1|CO448516
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|37401251|gb|CF637988.1|CF637988
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|211222467|gb|FL437623.1|FL437623
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|87155501|gb|DY400290.1|DY400290
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|194716931|gb|FK934090.1|FK934090
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCTTGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|30307203|gb|CD001876.1|CD001876
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|213188201|gb|FM181912.1|FM181912
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|60399031|gb|DN231847.1|DN231847
EST:     CTATGGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|60395817|gb|DN228687.1|DN228687
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|24767815|gb|CA402951.1|CA402951
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCAGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|211309921|gb|FL436450.1|FL436450
EST:     ATTGGGGAGGGCATGACACGTAGAGGACCATTCGGATGGT-TCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: ATTGGTGAGGGCATGACACGTAGA-GACCATTCGGAT-GTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|6563648|gb|AW231375.1|AW231375
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|4646712|gb|AI491575.2|AI491575
EST:     CTATTGGTGAGGGCATGGCACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|13236999|gb|BG355013.1|BG355013
EST:     CTATTGGTGAGGGCATGACACGTAGAGGCCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|6539106|gb|AW225245.1|AW225245
EST:     GAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: GAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|60396754|gb|DN229618.1|DN229618
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|211019798|gb|FL053491.1|FL053491
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|211107575|gb|FL066804.1|FL066804
EST:     ACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: ACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|32933748|gb|CF038560.1|CF038560
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|32942169|gb|CF046988.1|CF046988
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
EST: gi|211222468|gb|FL437624.1|FL437624
EST:     CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG                         CTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC
genomic: CTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 509

AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 752

AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 658

AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 540

AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAGgtacatacta ... tctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG
                           aattgac  putative branch site (score: 540)
                                   tctgctgttttctctt  CT-rich tract
                        atgaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatactatgagtccatgttatttttgataagggagtccatagtctttgctacccttcagacatgatgtgcaagatgaattgacatctgctgttttctctttcagCTTTATGCCAACTACGCAATTGGAAAGGATGTTCAGGCCATGAAGGCAGTCGTTGGAGAGGAGGCACTCTCGTCTGAGGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT