Sequence
atgc intronic sequence ATGC exonic sequence...aaataatttttgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g48740.1 (Oryza sativa), 3'ss of exon 10
aaataatttttgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatc-catagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
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-------------------------gtatgagattatttgaatgagcattt---gtgtctgtctccaaatgaattgggcacttacatcctttctcatgcagATGGGTACTTCTTGAAGTACTGGACAAAGTTTCTCCAGGATCTGTCAATTGGAAGCTGGCCTCGAAACCTCCAATTAAACTACCATTCAGGAAATTGGAG
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G010937_T01 (Zea mays), 3'ss of exon 10
aaataatttttgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttt-tccctagctttcttgatccatagtttctcatgt-atgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
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-------------------------------------gtaataagacatgcgatagattctgtctctaaatgatttggttattaatgtccattttgatgcagATGGGTACTTCTTGAAGTGCTTGACAAGGTGTCTCCTGGATCTGTCAATTGGAAGCTGGCAACAAAACCTCCAATTAAATTGCCATTTAGAAAACTGGAG
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G382341_T01 (Zea mays), 3'ss of exon 10
aaataatttttgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatccatagtttctcatgt-atgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
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---------------------gtaataagacatgtgttacattctgtctttttc-----tttctctaaatgatctggttattaatgtccattttgatgcagATGGGTACTTCTTGAAGTGCTTGACAAGGTGTCTCATGGATCTGTCAATTGGAAGCTGGCATCAAAACCTCCAATTAAATTGCCATTTAGAAAACTGGAG
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G556845_T01 (Zea mays), 3'ss of exon 9
aaataatttttgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
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---------------------gta-agacacatttgtagcaaaaaaaatttttttggtatatatgttgctacctca--ccggagtg----gtatttgcagATGGGTTTTGCTAGAGGTTCTTGACAAAATTTCTCCAGGGTCAGTTAACTGGAAGCATGCATCCAAACCACCAATCATTATGCCGTTTAGAAAGGTTGAA
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G46580.1 (Glycine max), 3'ss of exon 9
aaataatttttgaattgga-aagcagaaacaattttatggaacttgatat-tttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
| | || || | | || | || | | || || || | || || || | | |||||| | | | ||| ||| ||||||||||| || |||||| | |||||| | | ||| ||||| ||||||||||| | |||| ||| |||||| |||| |||||||||||||||||||||
ataccatgttgggaaaaattaaatgaatgtgatatca--aaatttaatttattaattcactaagttcttacgtgcttgatttgttttactttatgcatgtagATGGATACTTTTAGAAGTGTTAGACAAGATATTTCCTGGATCAGTTAACTGGAAACATGCAACAAGACCTCCAATTAGAATGCCATTCAGAAAAGTAGAG
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA14G02090.1 (Glycine max), 3'ss of exon 10
aaataatttttgaattggaaagcagaaacaatttta----tggaacttgatat-tttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
||| | ||||| ||| | | | || || || | || || || | ||||| | | | ||| ||| ||||||||||| || |||||| | |||||| | | |||| |||| ||||||||||| | |||| ||| |||||| |||| |||||||||||||||||||||
-----tccactgattgggaaaaattaaatgaatgtgatatcaaaatttaatttattaattcactaagttcttatgtgtttgatttcttttactttatgcatgtagATGGATACTTTTAGAAGTGTTAGACAAGATATTTCCAAGATCAGTTAACTGGAAACATGCAACAAGACCTCCAATTAGAATGCCATTCAGAAAAGTAGAG
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G41810.1 (Glycine max), 3'ss of exon 5
aaataatttttgaattggaaagcagaaacaattt---tatggaacttgatattttgcaa--gcttttccctagctttcttgatccatagtttctcatgt-atgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
||| | ||||| ||| | | ||| || || || || | | || || | ||||| | | | | ||| ||| ||||||||||| || |||||| | ||||| | | |||| |||| ||||||||||| | |||| ||| |||||| |||| ||||||||||||||||| |||
------ccactgattgggaaaaattaaatgaatgtgatatcaaaatttattttatcaattcactaagttcttatgtgtttgattccttttactttatgccatgtagATGGATACTTTTAGAAGTGGTAGACAACATATTTCCAAGATCAGTTAACTGGAAACATGCAACAAGACCTCCAATTAGAATGCCATTCAGAAAAGTCGAG
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G55400.1 (Arabidopsis thaliana), 3'ss of exon 9
aaataatttttgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
||| || ||| | ||| ||| ||||| || | ||| | || || | || || ||| | || | | | | || || |||||||||||| || ||||||| |||| ||||| | |||||| || ||||||||||||| || |||||||| || ||||||||||| || ||||||||||||
--gtaagcatt----tggtatgca-aaataattt-ata-atcttttggtcctgaaacgtatta--taagtttttcaatactgaatatttc-tg-atgcagATGGATTCTTCTGGAAGTTGTTGATAAGGTCTATCCAGGCTCAGTTAACTGGAAGCAGGCTTCAAAACCACCAATTAAGATGCCGTTTAGAAAAGTAGAG
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT4G26700.2 (Arabidopsis thaliana), 3'ss of exon 10
-----------------------------------------aaataatttt--tgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
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gtaatctttattttgagcttatagtaaatcaagcaattagtagaaaattttcctgcagttgatgac-gttgcatttggaaaatactgaaaacgctctttggtcctgatgccttttgtttgttc-catttactattttatgcagATGGATTCTTCTTGAGGTTCTTGACAAGGTCTCTCCCAGTTCAGTCAACTGGAAGCATGCTTCCAAACCACCGATTAAGATGCCGTTTAGAAAAGTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
tcttgat putative branch site (score: 4)
tttctcat putative PPT
atagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaataatttttgaattggaaagcagaaacaattttatggaacttgatattttgcaagcttttccctagctttcttgatccatagtttctcatgtatgcagATGGATACTCTTGGAAGTGCTTGACAAGGTTTCTCCAGGATCTGTTAACTGGAAGCGTGCATCAAAACCTCCCATTAAGATGCCATTCAGAAAAGTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
aaataat
- - - - - - - - -gaaagca
- - - - - - - - - - - - -aaacaat
- - - - - - - - - - - - - - - - - - - - - - - - ttttgca