Sequence
atgc intronic sequence ATGC exonic sequence...catttaatgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
catttaatgc--gtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgc--agGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
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---ttcgtgctatcacaataattgttttcctacactttgta-cacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G102163_T01 (Zea mays), 3'ss of exon 7
catttaatgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaat-tgtttatttgc--agGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
||| | | | | ||| | ||| |||||| |||| || | |||| || | ||| ||| || ||||||||||| ||||||||||||||||| ||||| ||||| || || || || |||||||| ||||| || ||||| || ||||| || ||||| ||
--tttcgaactaaaccgctacaaataaaaaaga-atggagtgagcagtaggcttgctttttttacttgactcgattttaatttttatctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGTCATCTTCTTGTGAAGAGCGACGTCTACAGTTACGGGGTTGTCTTGCTGGAACTTCTATCAGGAAGGAAG
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G32640.1 (Glycine max), 3'ss of exon 8
---catttaatgcgtattttaggtgtttgtt-tgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
| | || | | | | || || ||| | | | ||| || | |||||| | | || | | | | | | |||||||||||||||| || |||||||| ||||| || ||| ||||||||||||||||||| || |||||||| || ||| ||||||| |||||| | || |||||
taagaaatggtgggactatgggaggtgcattctgtttttcatgcattacaaattccaggtttttaatttgatgccttttc----tctgatctttaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTTGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G35390.1 (Glycine max), 3'ss of exon 8
-catttaatgcg--tattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
| | || | | | ||||| | | | ||| | | ||| || | ||| | | |||| || | | | |||||||||||||||| || |||||||| ||||| || ||| |||| |||||||||||||| || |||||||| || ||| ||||||| |||||| | || |||||
agaaatggtgggactgtgggaggtgcattctgtttttttgtgcattacaaattccaggttttaatttgatgccttttct---atctgatcttcaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G04700.1 (Glycine max), 3'ss of exon 5
catttaatgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgttta--tttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
| | || | | |||| || ||| | | || | || | || | ||| || || || | | || | |||||||||||||||| || |||||||||||||| || ||| |||| || ||||||||||| || |||| ||| || ||| ||||||||||||| | || ||||||
cccgtggcttataaatcatgtgtg-attaaaatcattttttgatgccattgtaaattcctagc-cttcaacttatgccatttctacctattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGCCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAGCTTCTGACAGGCAGAAAA
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G19030.1 (Glycine max), 3'ss of exon 6
catttaatgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgttta--tttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
| || ||| |||| || ||| | | || | || | | | ||| || || || | || | |||||||||||||||| || |||||||||||||| || ||| |||| || ||||||||||| || |||| ||| || ||| ||||||| ||||| | || || |||
tgtccgtggcttataaattgtgtg-attaacatcattttttgatgccattgtaaattcccagc-cttcaacttatgccatttctatgcattcaattttgcagGTATGTTGCCCCAGAATATGCAATGACAGGTCATTTACTCGTTAAAAGTGATGTTTATAGTTTTGGTGTTGTGCTGCTTGAACTTCTAACCGGCAGGAAA
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G20300.1 (Arabidopsis thaliana), 3'ss of exon 7
catttaatgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
|| ||| ||| | || | | |||| || | | |||| | | |||| ||| |||||| || |||||||| |||||||||||||||||||| ||||| ||||| ||||| || |||||||| || || | || |||||||| | || |||| |
---------------gtaaa-atttctttccaactcaaatatgatgaata-cagacactctggacttacagtgactaccctggaaataattt-----cagGTACGTGGCTCCTGAGTATGCAATGACGGGGCATCTCCTTGTTAAAAGCGATGTCTATAGTTATGGTGTAGTTCTACTAGAGCTTCTAACCGGTAGAAGA
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
catttaatgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggattta--aattgtttatt--tgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
|| ||||| | | | || | | | | ||||| | ||| ||| | | | | | ||| |||| || | ||||||||||| || |||||||| |||||||| |||||||||||||| || |||||||| |||||||| || || ||| | || ||||| ||||||||| | |||
---ttctcttgtattctcgtttcttctattttttagatatctttggc-tggaccgctagcgttgttacttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S43_35V6.1 (Physcomitrella patens), 3'ss of exon 2
catttaa-tgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttg-tggggatttaaattg--tttatttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
| || | | | || | | || | ||| || | ||| ||| ||| || | | || || | | | | ||| || | ||||||||||| || || || || || ||||| |||||| ||||||| || |||||||| || |||||||| || ||| | || ||||| || |||||| |||||
ctttcaccttcacatctgaatatttaggatgtattttga----ccagactggtaaggttgtgtcttgattattgacttacggtagtagttgatttcaactgcagGTATGTGGCCCCGGAGTACGCTATGACAGGGCATTTACTTGTGAAGAGTGATGTTTATAGTTATGGAGTGGTGCTTCTGGAGCTCCTTTCTGGACGAAAA
upper sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
catttaatgcgtattttaggtgtttgtttgt-gccatgtatctcaagaatggc--aagcttttaacacttttctttgtggggatttaaattg--tttatt-tgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
| ||| || | ||||| || | || || | | | | ||| ||| || | |||||| | || ||||||||||| || ||||||||||| |||||||| || || ||||| || || || |||||||| |||||||| || | ||||| ||||| || || || |
------accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
ttttaac putative branch site (score: 2)
tttattt putative PPT
atttaaattgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttaatgcgtattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - ccatgta
- - - - - - - - - - - - - - - - - - - - -tcaagaa
- - - - - - - - - - - - - - - - - - - - - - - - -ggcaagc