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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC

Basic information

species Zea mays
transcript GRMZM2G088231_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 3
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcat----gagctttataattc--ttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
               ||||  |  | || || |  | |  ||    | | |        || |||||| |||| | |     | |||||  ||||   |||||||||| ||||| || ||||| || ||||| ||||| ||||||||||| || |||||||||| ||| ||||| ||||||||||| || ||||||||||||||||
-----------gtgtgtgccaacacaatattattttcattat----ctggtaggttcaaataaaaatggatttattactgtggtgcttttgaattaaattttgtagTTCGAAGCTGCGTGGGCACTTACAAACATTGCATCTGGCACTTCGGAGAATACAAAGGTTGTCATTGATCATGGGGCTGTACCAATATTTGTGAAGCTTC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G04430.1 (Glycine max), 3'ss of exon 3
-tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
 ||| |   |||     ||| |  |   |||||  ||     |      | || |  | | ||         |  | ||  | | | |  || |||  |||||||| || || |||||||||||||| || || ||||| ||||| || ||||| ||||  || ||||| |||||||| ||||| |||||||| ||||| |
gttttgt-tttattccctgcattggaagtttttgtgtggt-gtagtgttgatgacatttgttg---------tgttgattggttctttgtttgtttgctagTTTGAGGCTGCGTGGGCTCTCACAAACATAGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCAGTTCCGATATTTGTCAAGCTAC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G03430.1 (Glycine max), 3'ss of exon 3
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgt--agTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
      | || ||   ||| |      ||||    | |         | |||| | |||||    || | |   | |||    || |  ||  |||||  ||||||| || || |||||||||||||| ||||| ||||| ||||| || || || ||||  || ||||| |||||||| |||||||||||||| ||||| |
------gtttgaa---tgccttttttcttttcatcttatttgtttttccttgt-ggtggatattcattagtaatttatgtcacttgttgtttgtttgtttagTTTGAGGCTGCGTGGGCTCTCACAAACATTGCATCTGGGACTTCTGAGAACACTAAGGTGGTAATTGATCATGGGGCAGTTCCTATATTTGTCAAGCTAC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G37180.1 (Glycine max), 3'ss of exon 4
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttt-tgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
      | || ||   | | |    | |||     | |         | |||| | | |||    || | ||  | |||    ||    || ||| | |||||||| || || |||||||||||||| ||||| ||||| ||||| || || || ||||  || ||||| || ||||| |||||||||||||| ||||| |
------gtttgaa---ttcctttttgctttgcatcttatttgtttttccttgt-ggtagatattcattagttatttatgtcacttgcttttgtttgtttagTTTGAGGCTGCGTGGGCTCTCACAAACATTGCATCTGGGACTTCTGAGAACACTAAGGTGGTAATTGATCACGGGGCAGTTCCTATATTTGTCAAGCTAC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G15480.1 (Glycine max), 3'ss of exon 3
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgc-tggatgaaaatgaatttctc-atgagctttataattcttttgt-agTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
                ||||  |     |   | | ||   | |      ||| |  | ||||  | |   | | |  ||  | | | |  || ||| || ||||||| || || ||||||||||| || ||||| ||||| ||||| || ||||| ||||  || ||||| |||||||| || || |||||||| || || |
------------gttttgctctattccctgcattggaagttttagtgtagtgtagtgtagatgggatttgttgtgttgattggttctttgtttgtttggttagTTTGAGGCTGCGTGGGCTCTCACGAACATTGCATCTGGAACTTCTGAGAATACCAAGGTGGTGATTGATCATGGGGCGGTGCCGATATTTGTCAAACTAC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 3
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattctt-ttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
      | ||   |  ||| |     | ||| |   | | ||       |  | |||        ||  |||||        | | ||||  || ||||||||||| || || |||||| | |||||||| |||||||| ||||| ||||| || ||||  || ||||| ||||| ||||| || || ||||| ||||| |
------gtttgttatctgccttgtttactttatttaatcgatatatttatctttgctt-------atttatttccttgactttgtttaatgtttgttgtagTTTGAGGCAGCTTGGGCTTTGACAAATATAGCTTCTGGAACTTCTGAAAACACCAAGGTGGTAATTGATCATGGTGCTGTCCCAATTTTTGTAAAGCTCC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G16143.1 (Arabidopsis thaliana), 3'ss of exon 2
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
      | ||    | |  ||| |  || | | |   |   ||      |||||    |||   ||| | ||     || | | | | |||       ||||||| || || |||||  | ||||| ||||||||||| |||||||| ||||||||||  || ||||| ||||| |||||||| || |||||  | ||  
------gtttggtggatcgttatgt-atctgtcat--attttgctagaattgtcttctgatactaattacttgtgtgtgtg-tgtgtgatttc-----agTTTGAGGCTGCTTGGGCATTGACAAACATTGCTTCTGGGACTTCAGAGAATACAAAGGTGGTCATTGAACATGGTGCTGTTCCGATTTTTGTTCAACTAT

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 3
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
 |  |   | | |   | | | |  | ||||  | ||  |||      | | | | |   |  | | || ||  | ||    || | || || |  |||||||||||| ||||||||||||||||| ||||||||||| || || || || || ||||  || ||||| ||||||||||| ||  | |||||||| ||||
gtatgttatgataccctccctcatggcttttaaattattcata---ttgatat-gatattttcagacgatttgattat----ttgaaaaatcct--gtagTTTGAAGCAGCATGGGCTCTCACAAACATTGCTTCTGGGACATCTGACAACACTAAGGTGGTAATTGATCATGGGGCTGTCCCGGTGTTTGTGAAACTTC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0005g01100.t01 (Vitis vinifera), 3'ss of exon 3
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatg----aatttctcatgagctt-tataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
 || |  ||   | | || |||  |   ||||||| | ||||      |  |    |  |||    |       ||| | ||   ||  | | | | || | |||||||| || || |||||||||||||| ||||||||||| || |||||||| || |||| ||| || || ||||| || ||||| || |||||||||||||
gtttgaact---aggctgtttattcctgtttttag-atccatttaaatgaagcatttatatgctcctcttttgttttgttatttactgatttgaattttatttagTTTGAGGCTGCTTGGGCTCTCACAAACATTGCTTCTGGAACATCAGAAAACACCAAGGTTGTAATAGATCATGGAGCAGTTCCGATTTTTGTGAAGCTTC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0077g01430.t01 (Vitis vinifera), 3'ss of exon 3
-tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
 ||||| | ||      || |||     || ||| || |  |   |    |||| | | | | ||  |   | | |||  |      | | | || | |||||||| || || |||||||||||||| ||||||||||| || ||||||||||| ||||  || ||||| ||||| || || || |||||||||||||| |
gtttgg-gattgttctttg-ttacattgttgtttggttatta--gcagttttgtagtttgtttaag-tacttatttcaataatggcttcaattttgtctagTTTGAGGCAGCTTGGGCTCTCACAAACATTGCTTCTGGGACATCAGAAAATACCAAGGTGGTAATTGATCATGGAGCAGTGCCAATATTTGTGAAGCTAC

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S63_171V6.1 (Physcomitrella patens), 3'ss of exon 3
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
  |  | ||   | |     |||   || |  ||     | ||||    |      ||  | |  ||| |  | ||     |   | |||   | |||||||||||||||| ||||| || ||||||||||| || || || || ||  | ||    |  || || ||||||||||| || || ||||||||  | ||  
-gtaacactctgatg-----taataaatctaatacctttcttgactatttgaagtatgagttatcatgtagatatctca--cacaagaatgtctctgtagTTTGAAGCCGCGTGGGCGCTTACAAATATTGCATCCGGAACGTCTGACCACACCCGCGTCGTGATCGACCATGGGGCCGTGCCCATATTTGTTCAACTCT

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|71440662|gb|DR821712.1|DR821712
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|211383277|gb|FK983407.1|FK983407
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATT-CCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTG
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTG
EST: gi|211385914|gb|FK983423.1|FK983423
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|28987202|gb|CB351514.1|CB351514
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|149111962|gb|EE191122.2|EE191122
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|87151836|gb|DY396625.1|DY396625
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|30087090|gb|CB885298.1|CB885298
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|76021460|gb|DT948630.1|DT948630
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|31664557|gb|CD573490.1|CD573490
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|78179900|gb|DV550273.1|DV550273
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|211385909|gb|FK983418.1|FK983418
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|18963328|gb|BM660373.1|BM660373
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|22490161|gb|BU050084.1|BU050084
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|211383281|gb|FK983411.1|FK983411
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|18963326|gb|BM660372.1|BM660372
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|6952404|gb|AW424472.1|AW424472
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|211385917|gb|FK983426.1|FK983426
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCA-AAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|211383287|gb|FK983417.1|FK983417
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCTGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|148946964|gb|EC892254.2|EC892254
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
EST: gi|12045741|gb|BF727880.1|BF727880
EST:     TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAG                         TTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT
genomic: TTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAAT

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: 374

AGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 159

AGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

AGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

AGAGGAGTCTCCCCCATCGAAGAAGTTATCAAAACAGGTGTAGTTCCAAGATTTGTGCAGTCTCTCACCAGAGAGGATTTCCCCCAGCTGCAGgtatgttgat ... tcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC
                                            ttcttttgt  CT-rich tract
                                     tttataattcttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggcgcttaaaaggtgcttaagcgattttttagtaaccatgaccccgttgtcgctggatgaaaatgaatttctcatgagctttataattcttttgtagTTTGAAGCCGCATGGGCTCTCACAAATATTGCTTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- tggcgct
- - - - - - - ggtgctt
- - - - - - - - - - - - - - - - - - - ccatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggatg