Sequence
atgc intronic sequence ATGC exonic sequence...aatacagttaagtctttttgtatgcaacagggtctcatgtataacttatctatgggtaagatgtactgtaacagtgtatgctattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 3
-------------------------------aatacagttaagtctttttgtatgcaacagggtctcatgtataactt--------atctatgggtaa-gatgtactgtaa--cagtgtatgctattttttatttg----ccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
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gtatgtattgtgttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacacattccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG
upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------aatacagttaagt--ctttttgtatgcaacagggtctcatgtata----acttatctatgggtaagatgtactgt--aacagtgtatgctatt--ttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
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gtatgtactttatcactactacaagatgattgtttcttaaacacaattggataaagcataatttactgcattttaattgatgaaaatgaataacaagctgaaaataaaatagttccatcttttctgcacttatcttgtgaacacaaaaactgttagataataccaggaatccatttcatggaatgtagTGTGGTCAATGGTGCGCTTGAATATCTTGCGAAGGATCTTGGAATTGCTGAAAATGCCGTCTTACAG-
upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------aatacagttaagt--ctttttgtatgcaacagggtctcatgtata----acttatctatgggtaagatgtactgt--aacagtgtatgctatt--ttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
|| | | | | | || | || | || ||| | | |||||||| | | | ||||| | | | | || ||| || || ||||| |||||||| |||||||| ||| | |||||||||||||||||||||||||| || ||||| |
gtatgtactttatcactactacaagatgattgtttcttaaacacaattggataaagcataatttactgcattttaattgatgaaaatgaataacaagctgaaaataaaatagttccatcttttctgcacttatcttgtgaacacaaaaactgttagataataccaggaatccatttcatggaatgtagTGTGGTCAATGGTGCGCTTGAATATCTTGCGAAGGATCTTGGAATTGCTGAAAATGCCGTCTTACAGG
upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G153704_T01 (Zea mays), 3'ss of exon 7
----------------------------------------------------------------------------------aatacagttaagtctttttgtatgcaacagg---gtctcatgtataacttatctatgggtaaga----tgtactgtaacagtgtatgctattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
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gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaataatgagctggaagtataacagttacatcttttctgcacttctgttgtggacacaaaaactgttagttaatagcatgaatc-cgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG
upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------aatacagttaagtctttttgtatgcaacagg---gtctcatgtataacttatctatgggtaaga----tgtactgtaacagtgtatgctattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG-----
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gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaataatgagctggaagtataacagttacatcttttctgcacttctgttgtggacacaaaaactgttagttaatagcatgaatc-cgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATG
upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 3
aatacagttaagtctttttgtatgcaacagggtctcatgtataacttatctatgggtaagatgtact-gtaacagtgtatgc-tattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
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--tgttcttttggcttcttgacatatatataactgctactactttttatttttaatcaatatcttcttgtttaagaactcgaacaatccctgtttggtttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGAAAATACTGTTATACAAG
upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 3
aatacagttaagtctttttgtatgcaacagggtctcatgtataacttatctatgggtaagatgtactgtaacagtgtatgctattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
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---------------------gtatgactaaatactacactgtttttatcttggtgtga----tcatggatgatgatgttctattg---gactgaatcagGGTGGTTAATGGTGCTCTTGAATATCTTGCTAAGGATCTTGGGATCGCCGAAAATACTGTTTTGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatctatgggtaagatgtactgtaacagtgtatgctattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
ctgtaac putative branch site (score: 3)
ttttttattt putative PPT
tatgctattttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatacagttaagtctttttgtatgcaacagggtctcatgtataacttatctatgggtaagatgtactgtaacagtgtatgctattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
aatacag
- - - - - - - - - -gtatgca
- - - - - - - - - - - - - - - - - tcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtatg