Sequence
atgc intronic sequence ATGC exonic sequence...ttggtgcaattgatttcattgtaaaatcttatttttgcatttggttcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g28090.1 (Oryza sativa), 3'ss of exon 1
ttggtgcaattgatttcattgtaa--aatcttatttttgcatttggttcatt---tgtttttcta-cacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
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------ggttctatttgagcataaccaattgcacttgcagatttgtcacaccaactattattctctcattttattttctgtgctaactcttttttgttgatggcagACTGAATGGACAAGGGAAGAGGATGAGAAGTTACTGCATCTTGCTAAACTCATGCCTACGCAGTGGAGGACAATTGCACCTATTGTTGGTCGAACACCAT
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AC203535.4_FGT001 (Zea mays), 3'ss of exon 1
ttggtgcaat-tgatttcattgta-aaatcttattt--ttgcatttggttcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
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-tgctctattatgggcttatggcataggtctttcttgtttgtcaccaagatgattgtttattgtttctctcactgtgctaactcatctatgttaattt---cagACCGAGTGGACAAGGGAGGAGGATGAGAAATTACTTCATCTTGCTAAACTCATGCCTACTCAGTGGAGGACAATTGCACCTATTGTAGGTCGAACACCAT
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G30870.1 (Glycine max), 3'ss of exon 1
ttggtgcaattgatttcattgtaaaatcttattt--ttgcatttggttcat-ttgtttttctaca-cctggggagtggtgatttaact--cctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
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----tgcattt--ttccatctacagcctttgtctacctctttttagtttttactatctagctatttcctaatgagtggtttttcaattgatgctttttgtgtgtagACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACACAGTGGAGAACAATTGCTCCAATTGTTGGCCGTACCCCTT
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G36600.2 (Glycine max), 3'ss of exon 1
ttggtgcaattgatttcatt-gtaaaatcttatttttgcatttggttcatt--tgtttttctacac-ctggggagtggtgatttaact---cctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
||| || || ||| | | | || | ||| | || | | | |||| || ||||| | || || | || || | || ||||||| ||||| |||||||| |||||||| |||||||||||||| ||||| ||||| || |||||||| ||||||||||| |||||||| ||||| ||||
-----gcattt--ttccatccacagcgtttgtcttccactttttagtttttactatctatctatttgctaatgagtgatttttcaatttgatgctttttgtgtgtagACTGAGTGGACGAGAGAAGAGGATGAGAAGCTACTTCATCTTGCTAAGCTTATGCCCACTCAATGGAGGACAATTGCTCCAATTGTTGGCCGTACCCCTT
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S641_1V6.1 (Physcomitrella patens), 3'ss of exon 1
ttggtgcaattgat--ttcattgtaaaatcttatttttgcatttggttcatttgtttttctacacctggggagtggtgatttaactc----ctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
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------taattaatgcttctcgggttagtattgcacgctagttagggtgattcttatttttcaggccggatgtgtctgttgaaaatctggaccttggtttgtgcagACGGAATGGACTAGAGAAGAGGACGAGAAACTCCTTCATCTTGCAAAACTTATGCCCACTCAGTGGCGAACTATTTCTCCCATAGTTGGTCGTACTCCAG
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ16246 (Selaginella moellendorffii), 3'ss of exon 1
ttggtgcaattgatttcattgtaaaatcttatttttgcatttggttcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
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---------------------------------------gtgaattgacttcctcttccttgcttcttttctcacggatttgcatttgtctgc----cagACGGAATGGACCCGCGAGGAAGACGAGAAGCTCCTTCACCTCGCCAAGCTCATGCCGACGCAATGGAGAACGATCGCTCCCATCGTTGGGAGAACTCCTG
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ17718 (Selaginella moellendorffii), 3'ss of exon 1
ttggtgcaattgatttcattgtaaaatcttatttttgcatttggttcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
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---------------------------------------gtgaatcgacttcctcttccttgcttcttttctcacggatttgcatttgtctgct----agACGGAATGGACCCGCGAGGAAGACGAGAAGCTCCTTCACCTCGCCAAGCTCATGCCGACGCAATGGAGGACGATCGCTCCCATCGTTGGGAGAACTCCTG
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ17861 (Selaginella moellendorffii), 3'ss of exon 1
ttggtgcaattgatttcattgtaaaatcttatttttgcatttggttcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
|| | | | | || || | | | | | | || | || | | | ||||| ||||||||| | || ||||| ||||| || ||||| || ||||||||||||||||| ||||||||||| || |||||||| ||||| | ||||||
----------------------------------gtgagtcgaatccctc---ttccctggatttctttttttctcacggatctgcctt-tccctgccagACGGAATGGACCCGCGAGGAAGACGAGAAGCTCCTTCACCTCGCCAAGCTCATGCCAACGCAATGGAGAACGATCGCTCCCATCGTTGGGAGAACTCCTG
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ16393 (Selaginella moellendorffii), 3'ss of exon 1
ttggtgcaattgatttcattgtaaaatcttatttttgcatttggttcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
| | | | | || || || | | | | | | | | | | ||||| ||||||||| | || ||||| ||||| || ||||| || |||||||||||||| || ||||||||||| || |||||||| ||||| | || |||
--------------------------------------------gtgagtcgaatccctcttccctggatttctttttatctcacagatttgcctgccagACGGAATGGACCCGCGAGGAAGACGAGAAGCTCCTTCACCTCGCCAAGCTCATGCCGACGCAATGGAGAACGATCGCTCCCATCGTTGGGAGAACACCTG
upper sequence: Vv14s0036g00510.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ17860 (Selaginella moellendorffii), 3'ss of exon 1
ttggtgcaattgatttcattgtaaaatcttatttttgcatttggttcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
| | | || | ||| | | | || || | | || | | | ||||| ||||||||| | || ||||| ||||| || ||||| || ||||||||||||| || || |||||||| || ||||||||||| || | |||||
---------------------------------------gtaaatcgacttcctcttccttgcttcttttctcatggatt---tgcattttgcctgccagACGGAATGGACCTGCGAGGAAGACGAGAAGCTCCTTCACCTCGCCAAGCTCATGCTGACGCAGTGGAGAACGATCGCTCCCATTGTGGGGAGACCTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
atttaac putative branch site (score: 3)
ctcctttattctttgc CT-rich tract
tttattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggtgcaattgatttcattgtaaaatcttatttttgcatttggttcatttgtttttctacacctggggagtggtgatttaactcctttattctttgcagACTGAATGGACCAGAGAAGAAGATGAGAAACTACTTCATCTTGCCAAGCTCATGCCAACACAATGGAGAACAATTGCTCCCATTGTTGGACGTACTCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
-tggtgca
- - - - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggagtg