Sequence
atgc intronic sequence ATGC exonic sequencegtatgatctctttctttctgtgccccgctggttcttaatatgacatctttttttaattgtactcttttattttgcttttaggttgtttggttactgctcttgttatgtgattgcctatatgttttctactcttctaacatgtgttctttttgagtggtgacagTCAATGATTGAGCTAAGCCGCACACAAGATGAGGAAGTAGGAGATGGAACAACATCTGTAATTGTTCTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 3'ss of exon 4
gtatgatctctttctttctgtgccccgctggttcttaatatgacatctttttttaattgtactcttttattttgcttttaggttgtttggttactgctcttgttatgtgattgcctatatgttttctactcttctaacatgtgttctttttgagtggtgacagTCAATGATTGAGCTAAGCCGCACACAAGATGAGGAAGTAGGAGATGGAACAACATCTGTAATTGTTCTTG
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-------------------------------------------------aatgaaactgcacgtagctcctaaaccttgagctcttttcttagccctattctcgatgctcagtcctgtattcctaatacttt------atgagttgtccatg--------cagTCTATGATTGAGCTAAGCCGCACACAGGATGAAGAAGTAGGAGATGGCACGACATCTGTTATTGTTCTTG
upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 4
gtatgatctctttctttctgtgccccgctggttcttaatatgacatctttttttaattgtactcttttattttgctt-ttaggttgtttggtta--ctgctcttgttatgtgattgcctatatgttttctactcttctaacatgtgttctttttgagtggtgacagTCAATGATTGAGCTAAGCCGCACACAAGATGAGGAAGTAGGAGATGGAACAACATCTGTAATTGTTCTTG
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--------------------------gtatgtggaacgttagatgttttctctctgttgagtactactgatgaaattattagtctgatgtgttaaattgccaatattttctgctaatgtatgaattagtacttaatctaactt----tcttgtcactctttggcagTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTCATTGTTTTAG
upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 4
gtatgatctctttctttctgtgccccgctggttcttaatatgacatctttttttaattgtactcttttattttgcttttaggttgtttggttactgctct-tgttatgtgattgcctatatgttttctactcttctaacatgtgttctttttgagtggtgacagTCAATGATTGAGCTAAGCCGCACACAAGATGAGGAAGTAGGAGATGGAACAACATCTGTAATTGTTCTTG
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------------------------------------------------------------acccgtatatataccctacca--tatttgtgtgctaatgtgcagtctatggttcatgttgtgagtcccatgtacttaattgtggttgtgtttaaatgt--gcagTCTATGATTGAACTAAGTCGTACACAAGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG
upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgatctctttctttctgtgccccgctggttcttaatatgacatctttttttaattgtactcttttattttgcttttaggttgtttggttactgctcttgttatgtg-attgcctatatgttttctactcttctaacatgtgttctttttgagtggtgacagTCAATGATTGAGCTAAGCCGCACACAAGATGAGGAAGTAGGAGATGGAACAACATCTGTAATTGTTCTTG
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------------------------------------------------------------------------------------gttttacttctgacctttctctatctattgttcttgttaaaattgttttacttatccatttttgactctggtgattgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgcctatatgttttctactcttctaacatgtgttctttttgagtggtgacagTCAATGATTGAGCTAAGCCGCACACAAGATGAGGAAGTAGGAGATGGAACAACATCTGTAATTGTTCTTG
ttctaac putative branch site (score: 1)
tatatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatctctttctttctgtgccccgctggttcttaatatgacatctttttttaattgtactcttttattttgcttttaggttgtttggttactgctcttgttatgtgattgcctatatgttttctactcttctaacatgtgttctttttgagtggtgacagTCAATGATTGAGCTAAGCCGCACACAAGATGAGGAAGTAGGAGATGGAACAACATCTGTAATTGTTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA