Sequence
atgc intronic sequence ATGC exonic sequencegttagttatgttgtagcgataccctttttctagggctgctgtaattgtctcttatcttcaaagctcacttccccctgatatcttagctaattagtaattcaaaattttatgatttgcttctagcagAATGAGACCCTTATAGCAATTAAAGCTCCACATGGGACCACTCTGGAAGTTCCAGATCCTGATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G041701_T02 (Zea mays), 3'ss of exon 9
gttagttatgttgtagcgataccctttttctag--ggctgctgtaattgtctcttatcttcaaagc---tcacttccccctgatatct-tagctaattagtaattcaaaattttatgatttgcttctagcagAATGAGACCCTTATAGCAATTAAAGCTCCACATGGGACCACTCTGGAAGTTCCAGATCCTGATGAG
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gtctggtttagtttagtggtttccaatgccatattaaatggattaactgttgctttaggccaaaataattttcttgatgtcaacatgtataatagattggtagttgacattttggttgtttgt-----gcagAATGAAACACTAATTGCAATTAAAGCACCTCATGGTACTACTCTTGAAGTACCAGATCCTGATGAG
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 9
------gttagttatgttgtagcgataccctttttct----------agggctgctgtaattgtctcttatcttcaaagctcact--tccccctgata-tcttagctaattagtaattcaaaatttta-tgatttgcttctagcagAATGAGACCCTTATAGCAATTAAAGCTCCACATGGGACCACTCTGGAAGTTCCAGATCCTGATGAG
|| || ||| | ||| | | || | || | | ||| | | | | || || | | | | || | ||| | || || || ||| || | || || | |||||||||| || || ||||||||||||||||| ||||| ||||| |||||||| || |||||||| ||
gtcattttttattgcattgcactcccaccttatcacttgttattgtaaacattgattttgctgtgttctcttgttaattctgattattgttattattagtattaagttttttgtttttattaatactagttcatttctgcaagcagAATGAAACTCTAATAGCAATTAAAGCTCCGCATGGAACCACCCTGGAAGTCCCCGATCCTGAGGAA
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G35850.1 (Glycine max), 3'ss of exon 9
------gttagttatgttgtagcgataccctttttctagggctgctgta-attgtctct--tatcttcaaagctcacttccccctgatatc-ttagctaattagtaattcaaaatttta-tgatttgcttctagcagAATGAGACCCTTATAGCAATTAAAGCTCCACATGGGACCACTCTGGAAGTTCCAGATCCTGATGAG
|| || ||| | ||| | | || | || | | |||| | | | | ||| | | | ||| | ||| ||| | || | || ||| || | || || | |||||||||| || | ||||||||||||||||| ||||| ||||| |||||||| || |||||||| ||
gtcattttttcttgcattgcactcccaccttatcacttgttatgataaacattgcttttgctgtgttctactgttaattctgattattattattaagttttttctttttattaatactagttcatttctgcaagcagAATGAAACTTTAATAGCAATTAAAGCTCCGCATGGAACCACCCTGGAAGTCCCTGATCCTGAGGAA
upper sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S38_356V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------gttagttatgttgtagcgataccctttttctagggctgctgtaattgtctcttatcttcaaagct--cacttccccctgatat-cttagc-taattagtaattcaaaattttatgatt--tgcttctagcagAATGAGACCCTTATAGCAATTAAAGCTCCACATGGGACCACTCTGGAAGTTCCAGATCCTGATGAG
|| ||| || | || | | || | | ||| ||| | | ||| | |||| | |||| | ||| | ||| | | | | | || ||| || | | |||||||||||| ||||| || || || || || | |||||| ||| |||||||||||||||| ||||||
gtgagcatagagtttctggtttggttccattttc-cgttgactgcattgtggcaactttgtgattcttcaagagcttttgtattgttgcttctctctgaaagacttgacataacttaagactaagtacttcggtattcttggtgtttgcagAATGAGACACTTATTGCTATCAAGGCCCCTCTTGGGACGACTTTGGAAGTTCCAGATCCAGATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccctgatatcttagctaattagtaattcaaaattttatgatttgcttctagcagAATGAGACCCTTATAGCAATTAAAGCTCCACATGGGACCACTCTGGAAGTTCCAGATCCTGATGAG
agctaat putative branch site (score: 3)
tttgcttct putative PPT
taattagtaattcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttatgttgtagcgataccctttttctagggctgctgtaattgtctcttatcttcaaagctcacttccccctgatatcttagctaattagtaattcaaaattttatgatttgcttctagcagAATGAGACCCTTATAGCAATTAAAGCTCCACATGGGACCACTCTGGAAGTTCCAGATCCTGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG