Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG

Basic information

species Physcomitrella patens
transcript PP1S14_433V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g07709.1 (Oryza sativa), 3'ss of exon 1
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
                                                                                   |    |   ||  | |   |  | | |  |||  ||     || ||  ||      | |  |  ||    || |   ||  |||   | | |   ||||||||||||||||| ||||| || |||||||| || ||| || ||||||| ||||| |||||    || ||||| ||||| ||  | |||||||| ||||
----------------------------------------------------------------------------------gtaagctccgttcctctcccgcatctcccctttgcag-----tggtctctttgcgcaggtgctaaggggaggaatcgcgtgtgtgtttgatttttgcagTCGCTGATCGCGGGGGAGGATTTCCAGCACATCCTGCGTCTGCTGAACACGAACGTGGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG

upper sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
                                                                  ||    || |   |   || |  | |  |   ||   || |  | |||       |  ||| ||  | ||  |  | |     || |   ||  | |  || |         |||||||||||||| || ||||| || |||||||| || ||| || ||||||| |||||||||||    || ||||| ||||| ||  | |||||||| ||||
------------------------------------------------------------------gtaaccttctcgctcgcttctcctctcctccattcccgtctc-cgattcgccttctcgtga-cgcctcctctgactga-----ctctcgttggcgcttctgtccccg-----cagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG

upper sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G062911_T01 (Zea mays), 3'ss of exon 1
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
                                                                                                  |    | |  ||  |       ||  | |||    |   | |   ||| | |||  || | ||||||    || | ||  ||||||||||| ||||| ||||| ||||||||||| || ||| || | ||||| ||||| |||||    || ||||| ||||||||| | |||||||| ||||
-------------------------------------------------------------------------------------------------gtaagagctcctccctaccccattttgtcatcacgggtcggcg---attagtctgacac-gcggttggcattggctttg--cagTCGCTGATTGCGGGGGAGGACTTTCAGCACATCCTGCGTTTGCTTAACACCAACGTGGATGGCAAGCAGAAGATCATGTTTGCCCTCACCTCCATCAAGG

upper sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgag-gttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
                                                                                |            | |      |    || |  || |  ||| || |  |  |  | |      || |||||| | || | | |  | |    ||     |||| ||| | ||   ||||||||||||||||||| | |||||| | ||||||||||| |||||    |||||||||||||||||| | ||||| || || |
-------------------------------------------------------------------------------atcagagaaccaagtatcgaacagaaagtttaggttatgtgttgattagggaatttttgat---gtttggctgtaattgtgtgatttttgttactgcatgtagTCTCTGGTTGCAAATGAGGAGTTTCAGCACATTTTGCGTGTGCTCAACACTAACGTTGATGGTAAGCAAAAGATTATGTTTGCCCTTACCTCTATCAAAG

upper sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
                                                           | |    | |  |   ||  |   ||||   |||||||| ||| |||| |      | |  ||| ||||         ||||||||||   | ||        || ||  | |||||   |||| ||| | ||   |||||||||||| |||||||||||||||||||| ||||| || |||||    || ||||||||||||||| | ||||| || || |
---------------------------------------------------------aatgtaatcgcgagtaagttgataaattttgcgttttttttgtttagtttatg-----tgaaattactgat---------gggttaattgaattttg--------tgttgttgattgtg--tagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG

upper sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G22780.1 (Arabidopsis thaliana), 3'ss of exon 1
-----gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttg-gtggcggt-tgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
      ||   | || ||  || |||  |   |||    |  |   |  || ||  |  || ||   |   || ||||  ||  |  ||||    ||    ||||  | |       |||||   ||      |      |  |  | |  |  ||||   |    ||  ||    || ||||   |||| ||  | |||   |||||||||||||| ||||| |||||| | || ||||| ||||||||    ||||| ||||||||||| |||||||| || ||||
gtacgattatcgttcttcaactcttgtctggttctccaattgc---tcgtgcttcattttgcgtatcgctcgt-ttttcattgctggttttgggattggagttttaagctcaaatgttttttgtattcccttacacgatttgcgactgacggatctgttttttttttttcgtattcgtgtgtgtgtagTCTCTAGTTGCGAACGAGGAGTTTCAGCATATTCTGCGTGTGCTCAATACTAATGTCGATGGGAAGCAAAAAATTATGTTTGCTTTGACCTCAATCAAGG

upper sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
                                                                               |   |    || ||||  ||| || |   |||||| ||  ||  |  || |||       |||  |||   ||| | |||  ||||      || ||  ||||| ||  | ||    ||||| ||||||||||||||||||||| | ||||| |||||||||||    || ||||| ||||||||| | || ||||| ||||
------------------------------------------------------------------------------gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggtt-------gtttgttgttatgttaatgaa-ttgg-----attttg--cagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG

upper sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 1
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
                                                                                                                           |||||  ||   | ||||   |||   |    ||  ||   |   | ||| |||| |||| ||| |      ||||||||| |||||||||||||||||| | ||||| || || || || || || ||||||||||| ||  |||| ||||| ||||
-------------------------------------------------------------------------------------------------------------------------gtatgattcttgtgttgggt--gttgaaataatcctccggc--gcctctgttttggc-agTCTCTGGTGAGCAATGAGGAGTTCCAGCACATTCTTCGTGTGCTCAACACGAATGTGGACGGGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGG

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|162230970|gb|FC407225.1|FC407225
EST:     GTNTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162235758|gb|FC411061.1|FC411061
EST:     CTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: CTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162202825|gb|FC379807.1|FC379807
EST:     GCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162217729|gb|FC393821.1|FC393821
EST:     GCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|208344587|gb|DC909146.1|DC909146
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|100450815|gb|CJ974453.1|CJ974453
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162221578|gb|FC397595.1|FC397595
EST:     TTTGCGCCATCGCCAGCTCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: TTTGCGCCATCGCCAGC-CTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162211535|gb|FC387615.1|FC387615
EST:     GTNTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|7583669|gb|AW699576.1|AW699576
EST:     ACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: ACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162221577|gb|FC397594.1|FC397594
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162223027|gb|FC399645.1|FC399645
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|19790327|gb|BQ041813.1|BQ041813
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162230971|gb|FC407226.1|FC407226
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162278921|gb|FC454972.1|FC454972
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|19781079|gb|BQ039654.1|BQ039654
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162278920|gb|FC454971.1|FC454971
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162211536|gb|FC387616.1|FC387616
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162213890|gb|FC390089.1|FC390089
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162217807|gb|FC394107.1|FC394107
EST:     CGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: CGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162223518|gb|FC399148.1|FC399148
EST:     GTNTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162223026|gb|FC399644.1|FC399644
EST:     GTNTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162223519|gb|FC399149.1|FC399149
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|162214369|gb|FC390088.1|FC390088
EST:     GTNTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
EST: gi|208378326|gb|DC923011.1|DC923011
EST:     GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATG                         TCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT
genomic: GTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACT

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 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 212

CCTTTCTGTTCTAGGCCCCTGTCGCCTCAGCGTTTGCGCCATCGCCAGCCTTTCGCTACACTTCGCTTCTTGCCGACCATGgtttgtgctc ... ttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG
            ggttaat  putative branch site (score: 212)
              ttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA