Sequence
atgc intronic sequence ATGC exonic sequence...tttccccttttggttttgaattgtttgatatttttcaatgcatgtcctgtatgatttgacatgtgttttattttgatgttgaattgcttccttctatcagGGGCCTGGAGGTCTATGGTGTGATGTGGATGTGGTTGAATTTGCTTATTTTGGTGCACCTGAGTTAGCTCCCAAAGAACAGTATTATACTGAGATTATGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0027g00520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G150212_T03 (Zea mays), 3'ss of exon 4
tttccccttttggttttgaattgtttgatatttttcaatgcatgtcctgtatgatttgacatgtgttttattttgatgttgaattgcttccttctatcagGGGCCTGGAGGTCTATGGTGTGATGTGGATGTGGTTGAATTTGCTTATTTTGGTGCACCTGAGTTAGCTCCCAAAGAACAGTATTATACTGAGATTATGG
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--------gtaggcacgattttgtttcatgtagtttacaaagttatttaagccatctgaatcacatacagtttcg--------ttgcattccataaacagGGACCTGGGGGTGTGTGGTGTGATGTTGATGTTGTTGAATTTTCTTATTATGGTGCACCAGCCCCAACACCGAAGGAACAACTTTATGATGAGCTTGTTG
upper sequence: Vv19s0027g00520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G078541_T01 (Zea mays), 3'ss of exon 3
--tttccccttttggttttgaattgtttgatatttttcaatgcatgtcctgtatgatttga-catgtgttttattttgatg-ttgaattgcttccttctatcagGGGCCTGGAGGTCTATGGTGTGATGTGGATGTGGTTGAATTTGCTTATTTTGGTGCACCTGAGTTAGCTCCCAAAGAACAGTATTATACTGAGATTATGG
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tgatttcaatctctaattagagtt--ttgacgttta--aacgtagtttaaacatcgtttaaacgtagttttaataacactgatttcatcgcgttccataaacagGGACCTGGGGGTGTGTGGTGTGATGTTGATGTTGTTGAATTTTCTTATTATGGTGCACCAGCCCCAACACCAAAGGAACAACTTTATGATGAGCTTGTTG
upper sequence: Vv19s0027g00520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G40700.1 (Glycine max), 3'ss of exon 2
--------------------------------tttccccttttggttttgaattgtttgatatttttcaatgcatgtcctgt-atgatttg--acatgtgttttattttgatgttgaattgcttccttctatcagGGGCCTGGAGGTCTATGGTGTGATGTGGATGTGGTTGAATTTGCTTATTTTGGTGCACCTGAGTTAGCTCCCAAAGAACAGTATTATACTGAGATTATGG
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gttcttggagttgtccaaattgaacctgcttgatttaattttggagtttgaaatattt-atatatcacaaacagttttaggttgttatctggtgcctaggatgcatttaaaatcaatgttcaatttgtgaatcagGGGCCTGGTGGAGTATGGTGTGATGTGGATGTGGTGGAATTCTCGTATTTTGGTGCACCAGAGCCAGTTTCAAAAGAGCAGCTGTACACAGAGATCGTAG
upper sequence: Vv19s0027g00520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G18300.1 (Glycine max), 3'ss of exon 2
-------------------------tttccccttttggttttgaattgtttgatattt-ttcaatgcat---gtcctg---tatgatttgacatgtgttttattttgatgttgaattgcttccttct--atcagGGGCCTGGAGGTCTATGGTGTGATGTGGATGTGGTTGAATTTGCTTATTTTGGTGCACCTGAGTTAGCTCCCAAAGAACAGTATTATACTGAGATTATGG
| ||| ||||||| | | |||||| | || || || | | | | | | | | |||| | | ||| || | | ||||||||||| || ||||||| ||||| |||||||| ||||| | |||||||||||||||||| || ||| ||||| ||| || || |||||| | |
gttctcagagatgtccaaattgaacccgcttgatttaattttgaagtttgaaatatttatacatcacaaacagttttaggttgttctctagtacctaggatgctttggtaatcaatgttcaatttgtgaaccagGGGCCTGGTGGAGTATGGTGCGATGTAGATGTGGTGGAATTCTCATATTTTGGTGCACCTGAGCCAGTTCCAAAAGAGCAGCTGTACACAGAGATTGTAG
upper sequence: Vv19s0027g00520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ25881 (Selaginella moellendorffii), 3'ss of exon 1
tttccccttttggttttgaattgtttgatatttttcaatgcatgtcctgtatgatttgacatgtgttttattttgatgttgaattgcttccttctatcagGGGCCTGGAGGTCTATGGTGTGATGTGGATGTGGTTGAATTTGCTTATTTTGGTGCACCTGAGTTAGCTCCCAAAGAACAGTATTATACTGAGATTATGG
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------------------------------gtaactagtgcatgtaaaaccgctctcggcttct-taactcgctggtgaagtaacagtttctctactcagGGGCCTGGGGGAGTTTGGTGTGATGTAGATGTGGTTGAATTCTCGTACTATGGCGCTTCGACCGTGACACCAAAGGAGCAAATTTACTCCGAGCTGGTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgtatgatttgacatgtgttttattttgatgttgaattgcttccttctatcagGGGCCTGGAGGTCTATGGTGTGATGTGGATGTGGTTGAATTTGCTTATTTTGGTGCACCTGAGTTAGCTCCCAAAGAACAGTATTATACTGAGATTATGG
ttttgat putative branch site (score: 4)
ttgcttccttctatc putative PPT
ttttattttgatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttccccttttggttttgaattgtttgatatttttcaatgcatgtcctgtatgatttgacatgtgttttattttgatgttgaattgcttccttctatcagGGGCCTGGAGGTCTATGGTGTGATGTGGATGTGGTTGAATTTGCTTATTTTGGTGCACCTGAGTTAGCTCCCAAAGAACAGTATTATACTGAGATTATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- tcccctt
- - - - - - - - - - - - - - - - - -caatgca
- - - - - - - - - - - - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcttc