Sequence
atgc intronic sequence ATGC exonic sequence...gaactgattttagcttctaagctgagtattgaaaattttgcgtttgggctttccatgtggattttggaatgtattttttgtcataaatataactttgcagGTTGAAGACAGTGAACTAGCAGATGTGGCTGCAGTTAGTGCAGGAAACAACTATGAAGTAGGATATATGATAGCTGAAGCTATGGGTCAAGTTGGCAGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 5
gaactga----ttttagcttctaagctgagtattgaaaattttgcgtttgggctttccatgtggattttggaat--gtattttttgtcataaatataactttgcagGTTGAAGACAGTGAACTAGCAGATGTGGCTGCAGTTAGTGCAGGAAACAACTATGAAGTAGGATATATGATAGCTGAAGCTATGGGTCAAGTTGGCAGAA
||| | | || ||| | | ||| | | | | | || | || | | || ||| ||| | || | | | | || ||||||||||||||||||||| ||||| || ||||| ||||| || ||||| ||||| ||||| ||| | || | |||||||||||||||||| | ||||| ||
gaattcaggagcattggctgccagtttgaatcgt---actcatccgctacagcactatttttg---cttgaaatttgaatctatcatattgcatgcaactttgcagGTTGAAGACAGCGAACTTGCTGATGTTGCTGCGGTAAGTGCTGGAAATAACTACGAAATTGGCAACATGATAGCTGAAGCTATGAACAAGGTTGGACGAC
upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------gaactgattttagc--ttctaagct-gagtattgaaaattttgcgtttgggctttcca-tgtggattttggaatgtattttttgtcataaatataactttgc---agGTTGAAGACAGTGAACTAGCAGATGTGGCTGCAGTTAGTGCAGGAAACAACTATGAAGTAGGATATATGATAGCTGAAGCTATGGGTCAAGTTGGCAGAA
| | || | | | || |||| || | |||| | || || | | | | ||| ||| | || | | ||| || |||| |||||||||||||||| || || ||||| |||||||| ||||| || ||||| |||||| | || |||||||||| || |||||| | | |||||||| |
gtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
--gaactgattttagcttctaagctgagtattgaaaattttgcgtttgg-gctttccatgtggattttggaatgtattttttgtcataaatataactttgcagGTTGAAGACAGTGAACTAGCAGATGTGGCTGCAGTTAGTGCAGGAAACAACTATGAAGTAGGATATATGATAGCTGAAGCTATGGGTCAAGTTGGCAGAA
|| ||||| | || | | ||| || |||| | | | | | | ||| |||| | || | | | || | | || |||||||| |||||||| || || ||||| |||||||||||||| ||||| ||||||||| | || ||||||||||||| |||||| | ||||| |
gataattgattcccgtttgaatcttattcatttcaacttttaagaatactattccctcttcaaaattttgaatatgttg---gactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggctttccatgtggattttggaatgtattttttgtcataaatataactttgcagGTTGAAGACAGTGAACTAGCAGATGTGGCTGCAGTTAGTGCAGGAAACAACTATGAAGTAGGATATATGATAGCTGAAGCTATGGGTCAAGTTGGCAGAA
atataac putative branch site (score: 3)
aatgtattttttgtca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaactgattttagcttctaagctgagtattgaaaattttgcgtttgggctttccatgtggattttggaatgtattttttgtcataaatataactttgcagGTTGAAGACAGTGAACTAGCAGATGTGGCTGCAGTTAGTGCAGGAAACAACTATGAAGTAGGATATATGATAGCTGAAGCTATGGGTCAAGTTGGCAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaata