Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcaattcagtaaaaaaaatacctcaaaaaactaaagattgacaatccctcatactttatactatcttttaaagtttgtgcttggatcaaacagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os05g10730.2 (Oryza sativa), 3'ss of exon 9
-------gtgagttcaattcagtaaaaaaaatac-ctcaaaaaact--aaagattgacaatccctcatacttt--------atactatcttttaaagtttgtgcttggatcaa---acagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
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gtgagccctgattcagattccctagtgcataccttctcaatatattcagaagtttgtcagacaagtgtggttgcactgaaaagaaaaaatcctcatttctggccatctttcaatctccagTGAGCGACGACGGCGAGAACTGGAGCGCCGGACAACGGCAGCTCTTCTGCCTGGCCCGGGTCCTCCTCCGCAGGAACAAGATCCTGGTCCTCGACGAGGC
upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G059159_T01 (Zea mays), 3'ss of exon 2
gtgagttcaattcagtaaaaaaaatacctcaaaaaactaaagattgacaatccctcatactttatactatcttttaaagtttgtgc----ttggatca-aacagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC---
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-----gtatgtgaagataaaattatacccaaatcaatttatatcctattaaagagaa-actaaacacaatccgttt--gttcatgcaaaataaaattgtggtagTGAGTGATGATGGCGATAACTGGAGTGCTGGACAGCGTCAGCTCTTCTGTCTTGGCAGAGTTCTACGCAGGA---ACAAAATTCTAGTTCTAGACGAGGCAAC
upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G113203_T01 (Zea mays), 3'ss of exon 9
gtgagttcaattcagtaaaaaaaatacctcaaaaaactaaagattgacaatccctcatactttatactatcttttaaagtttgtgc----ttggatca-aacagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
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-----gtatgtgaagataaaattatacccaaatcaatttatatcctattaaagagaa-actaaacacaatccgttt--gttcatgcaaaataaaattgtggtagTGAGTGATGATGGCGATAACTGGAGTGCTGGACAGCGTCAGCTCTTCTGTCTTGGCAGAGTTCTCCTACGCAGGAACAAAATTCTAGTTCTAGACGAGGC
upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G20770.2 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------------------------gtgagttcaa---ttcagtaaaaaaaatacctcaaaaaactaaag------attgacaatccctcatactt---tatactatcttttaaagtttgtgcttgg---atcaaacagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
|| ||||| ||| | | | | ||||| ||| ||| | | | | || || || |||| | || | | |||||||| ||||| || | || ||||| || || ||||| || || || |||||| |||| ||||| ||||| |||||||| |||||||||||||||||
gtgagtaaacttctagccaattctctctgcagccttgggcaagaatctattgctgctttactcttttgaggtttaactttaggaggaattcaaaatcatagttgttcttacatgttgtacttttaaagcattcaattcgcaaattaagaaattggaacaatttagctattgaagtctaattctgacaagttatacagTGAGTGATGAGGGAGGAAATTGGAGCTTGGGACAGCGCCAACTGTTTTGTCTTGGAAGAGTACTACTTAAGAGGAACAGAATTCTTGTTCTAGATGAAGC
upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G20780.1 (Glycine max), 3'ss of exon 11
gtgagttcaattcagtaaaaaaaatacctcaaaaaactaaag-attgacaatccctcatactttatactatcttttaaagtttgtgcttg---gatcaaacagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
|| | || | ||| ||| || | | | | | ||| | || |||| | || || | || || | ||| | || | ||||||||| ||||||||||| |||||||||| || || || || ||| | || || ||| |||| || || ||||| |||||||| |||||||| ||||||||
--gactgcatattagtcaaattaaaattttacacatataatgtatcaacaaacaaaaat-tttactcctgactgaaatagtctaattctgaccaacttaacagTGAGTGATGAAGGTGAAAACTGGAGTGTGGGACAGCGTCAACTCATATGTCTCGGAAGAGTGCTTCTTAAGAGGAACAGAATTCTTGTTCTGGATGAAGC
upper sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G20360.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------gtgagttcaa--ttcagtaaaaaaaatacc--tcaaaaaactaaagattgacaatccc---tcatactttatactatcttttaaagtttgtgcttggatc---aaacagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
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gtgagttaacaaacctgaagccaacaatctgatgtacttttatataagtcactattctactctttcaacattaagtaaaatacaaagtaatcatatagttctgcatttttacccaaagatcttgcaacaaataaaccattgaagtctaattctgagttgttattcagTGAGTGATGAAGGTGGAAATTGGAGCTTGGGACAACAGCAACTGTTTTGTCTTGGAAGAGTACTACTTAAGAGGAACAGAATACTTGTTCTAGACGAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacaatccctcatactttatactatcttttaaagtttgtgcttggatcaaacagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
gattgac putative branch site (score: 3)
atactttatactatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcaattcagtaaaaaaaatacctcaaaaaactaaagattgacaatccctcatactttatactatcttttaaagtttgtgcttggatcaaacagTGAGCGATGAAGGTGAGAACTGGAGTGCTGGGCAACGCCAGCTCTTCTGCCTTGGACGAGTTCTACTCAAGAGAAACAGAATCCTTGTTCTAGATGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC