Sequence
atgc intronic sequence ATGC exonic sequence...ccatcttaggcagctggtatttttttacactgttactttgatgtatcacttatattttcatgagttgtcattgttcaaatttactgtcttccaattgtagGATGCTGTGGAATATGCTGAATGTGAAGCTGTTGTCAAAGACTGTCCTCTGTTTCGAGAGGCAATGAAGAAGAGGGGTGTGGAGGATATGGACCTTGTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 4
ccatcttaggcagctggtatttttttacactgttactttgatgtatcacttata--ttttcatgagttgtc--attgttcaaatttactgtcttccaattgtagGATGCTGTGGAATATGCTGAATGTGAAGCTGTTGTCAAAGACTGTCCTCTGTTTCGAGAGGCAATGAAGAAGAGGGGTGTGGAGGATATGGACCTTGTGA
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---tttccgatatttatgcttgtattacagc-ttgaactgttttttcttttgaagttttttagaaccttttggagcgctcagttcaaatttctatatttcacagGATGCTATGGAGTATGCTGAATGTGAAGCTACTGTCAAAAGCTATCCTCCATTTATTGAAGCTATGAAGAGAAGAGGTGTAGATGACATGGAACTTGTCA
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G09290.1 (Glycine max), 3'ss of exon 2
ccatcttaggcagctggtatttttttacactgttactttgatgtatcacttatattttcat---gagttgtcattgttcaaatttactgtctt--ccaattgtagGATGCTGTGGAATATGCTGAATGTGAAGCTGTTGTCAAAGACTGTCCTCTGTTTCGAGAGGCAATGAAGAAGAGGGGTGTGGAGGATATGGACCTTGTGA
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----attcaggatctttagtctttacatatttgtattttattttctt-tttatgtcgtaagttgaaattttcaattccgtaaggttctattctatccatcttcagGATGCTATGGAATATGCAGAATGTGAAGCTGTTGTTAAAGATTTCCCTCCATTTAGAGAGGCTATGAAGAAAAGGGGCATTGAAGACATGGATCTTGTAA
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 3
ccatcttaggcagctggtatttttttacactgttactttgatgtatcacttatattttcatgagttgtcattgttcaaattt---actgtct-tccaattgtagGATGCTGTGGAATATGCTGAATGTGAAGCTGTTGTCAAAGACTGTCCTCTGTTTCGAGAGGCAATGAAGAAGAGGGGTGTGGAGGATATGGACCTTGTGA
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--aaattggattcccaagctttgttttgaaagataatcagaaatgtggagttt-ttttaagctgctgcaatc-ctcaattccctaataatctctctatcttcagGATGCTGAGGAATATGCAGAATGCGAGGCTGTTGTCAAAAGTTTTCCCCCATTTATAGAGGCTATGAAGAAAAGGGGTATTGAAGACATGGACCTTGTAA
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S9_129V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------------------------ccatcttaggcagctggtatttttttacactgtta--ctttgatgtatcacttatattttcatgagttgtcattgttcaaat----------ttactgtcttccaattgtagGATGCTGTGGAATATGCTGAATGTGAAGCTGTTGTCAAAGACTGTCCTCTGTTTCGAGAGGCAATGAAGAAGAGGGGTGTGGAGGATATGGACCTTGTGA
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gtacttttgctctacttctacattagccgattaatttactaaacgattgagtgattggttgattcttatctaatcttgtgacaagtacttgcggcgcagatcttcgatgcctatgtcctaccaatatgagagttaattttgcaaatgattttttcttgtctgtgttgggatggcagGATGCTGTGGAGTATGCTGAATGTGAAGCACTTGTAAAAGAGCATCCAGCTGCCATTGAAGCCATGAAAAGAAGGGGGATTTACGACATGGATCTTGTTA
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------ccatcttaggcagctggtatttttttacact--gttactttgatgtatcactt----atattttcatgag-----ttgtcattgttc--------aaatttac----tgtcttccaattgtagGATGCTGTGGAATATGCTGAATGTGAAGCTGTTGTCAAAGACTGTCCTCTGTTTCGAGAGGCAATGAAGAAGAGGGGTGTGGAGGATATGGACCTTGTGA
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gtaggggtgctaagtctctgtagtagtc-gttagttttctcatttactaggtggcacgaagttaattctttgagaagtgcctgtgggggcttttatcactgttctgtaagtgacttttacaattcgtgctgcgctgtcagGATGCTGTGGAGTATGCTGAATGTGAAGCAACTGTGAAAGAGCATCCGTCTTTCGTTGAAGCCATGAAGAAACGGGGTATCGAGGATATGGATCTTGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacttatattttcatgagttgtcattgttcaaatttactgtcttccaattgtagGATGCTGTGGAATATGCTGAATGTGAAGCTGTTGTCAAAGACTGTCCTCTGTTTCGAGAGGCAATGAAGAAGAGGGGTGTGGAGGATATGGACCTTGTGA
ctgtcttcc CT-rich tract
attgttcaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatcttaggcagctggtatttttttacactgttactttgatgtatcacttatattttcatgagttgtcattgttcaaatttactgtcttccaattgtagGATGCTGTGGAATATGCTGAATGTGAAGCTGTTGTCAAAGACTGTCCTCTGTTTCGAGAGGCAATGAAGAAGAGGGGTGTGGAGGATATGGACCTTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
ccatctt
- - - - -gcagctg
- - - - - - - - - - - - - - -ctgttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgtc