Sequence
atgc intronic sequence ATGC exonic sequence...gtcattgtcttctgttgcataatcttagtcatttgttgctctgtctccagcaagtgaacgaaagtgtactaacatgtattctcaatttttgtccctacagAAGCGTGATGACGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGTGTTG
Basic information
species | Glycine max |
transcript | GLYMA20G25830.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 4
gtcattgtcttctgttgcataatcttagtcatttgttgctctgtctccagcaagtgaacgaaagtgtac-taacatgtattctcaattt---ttgtccctacagAAGCGTGATGACGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGTGTTG
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----gagaattgtgcatcattggtcttgttataaatatcataaaagagagaacaaaacctgtagtttgcatgggattcatactctgttccacttaatcttgcagACCCGTGATGATGCTAGGCAATTTATGAAGTATCTTCACCCTGATCTTGGTGTTG
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G095757_T02 (Zea mays), 3'ss of exon 4
gtcattgtcttctgttgcataatcttagtcatttg-ttgctctgtctccagcaagtgaacgaaagtgtactaacatgtattctca--atttttgtccctacagAAGCGTGATGACGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGTGTTG
|| | | | | | |||| | || | | |||| | ||| | || | | |||| ||| | ||||| | |||| |||||||| ||| | || || ||||||| ||||||||||||||||||||| |
-acagtattgcagcaagtcagagttcagtcgcaagattttaaagagtagagcaggaaaactta-gtatggcatttcatattttcattaactttgttt-tgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 4
--gtcattgtcttctgttgcataatcttagtcatttgttgctctgtctccagcaagtgaacgaaagtgtactaacatgtattctcaatttttgtccctacagAAGCGTGATGACGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGTGTTG
||| | | || | || || | || | || | | ||| | ||| | ||| | ||||| | |||| |||||||| ||| | || || ||||||| ||||||||||||||||||||| |
atttcagcaagtcagacttcaatggcaaagattttaaagagaagagcggcaaaatgtagtcatta-tgtcatttcatattttcatgaactttgttt-tgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
upper sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 5
gtcattgtcttctgttgcataatcttagt--catttgttgctctgtc-tccagcaagtgaacgaaagtgt-actaacatgtattctcaatttttgtccctacagAAGCGTGATGACGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGTGTTG
||| || || || ||| || || | | ||| | | ||||| | || | |||| ||| | | | ||||| |||||||| ||||| || || ||||||||||| |||||||||||||||||||
---tgtgtttttccctgaatttccttgacaccaattatggatctttggtatgatttccagttaaaagtattgatagtagtctttctgaatctct-catttccagAAACGTGATGATGCTCGGCAATTCATGAAGTTTCTCCATCCTGATCTTGGTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccagcaagtgaacgaaagtgtactaacatgtattctcaatttttgtccctacagAAGCGTGATGACGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGTGTTG
tactaac putative branch site (score: 0)
tttttgtccct putative PPT
tattctcaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcattgtcttctgttgcataatcttagtcatttgttgctctgtctccagcaagtgaacgaaagtgtactaacatgtattctcaatttttgtccctacagAAGCGTGATGACGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGTGTTG
- - - -tcttctg
- - - - - - - -tgcataa
- - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - -gcaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtat