Sequence
atgc intronic sequence ATGC exonic sequence...aggttgattttttatacaacaactagttgctgtaattgcttattaccttacctatctattaagttcatccgatcctaagaatatatctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
Basic information
species | Glycine max |
transcript | GLYMA16G28290.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 6
--aggttgattttttatacaacaactagttgctgtaattgcttattaccttacctatctattaagttcatccgatcctaagaatatatctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
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tcaagtgttattattataaatgtttaagtggtcttgactcatggctacataatatgatggacatatg-actcatagctaactaccactatgctcaatc-cagGGGCAAAGTAGCCGAAGGTATTGATTTTGATCGACACTATGGCAGACTTGTGATCATGTTTGGTGTTCCTTTCCAGTACACACTCAGCAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G097605_T02 (Zea mays), 3'ss of exon 1
-------------------------------------------aggttgattttttat-acaacaactagttgctgtaattgcttattaccttacctatctattaagttcatc-cgatcctaaga-atatatctacttgtt---------------tgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
| || || ||| || | ||| || | | | || | || | | || || || | || | || |||| ||| | |||| | |||||||| || |||||||||||||| ||||||||||| || |||||| || |||| |||||||||||||||||||| || |||||||| ||
gttggtccaccttattattttgcgttctgaaagcaaccttccaaaatttatatttgatcatgtcaaataatcagtaatgtgactgactatgtgatatagataaaaatgttgtcgccattgtaagctatagtttcacttttgctaacacttaactaatgcagGGGCAAAGTTGCTGAAGGTATTGATTTTGATCGGCACTATGGCAGATTAGTTATCATGTTTGGTGTTCCTTTCCAGTACACATTGAGTCG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------------------------------------------aggttgattttt-tatacaacaactagttgct--gtaattgcttattaccttacctatctattaagttcatccgatcctaagaatatatc-tacttgt-ttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
||| | || | | | | | |||| | || | | | | || | | | || || || | | | || | || ||| |||||||| || |||||||||||||| ||||||||||| |||||||| |||| || | |||| || || || || || || |||||||||||
gtaaaatttttatttttgaatggtagatggtttgggaattcattgcaatgcgtctttggttctgcttctttgtttctgtattataatactggaattgtctcttctctcctattcttggttggttaacaaatattaaagaggtttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 7
--aggttgattttttatacaacaactagttgctgtaattgcttattacc-ttacctatctattaagttcatccgatcctaagaatatatctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
| | | | | | | ||| || | | || || || ||| | | ||| ||| ||| ||| | ||||||||| || || ||||||||||| |||||||||||||||||||| || |||| |||||||||||||||||||| ||||||||||||||||
ggggaatcccctgatcccctggtatgaactgcataaagggatgggggtgattgagggtccatcaagatga---gattaaaagtttatttctgcactgttgcagGGGGAAAGTAGCTGAAGGTATTGATTTTGATCGACATTATGGAAGATTAGTGATCATGTTTGGTGTTCCTTTCCAATACACATTAAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttacctatctattaagttcatccgatcctaagaatatatctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
accttac putative branch site (score: 3)
tctactt putative PPT
taagaatatatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggttgattttttatacaacaactagttgctgtaattgcttattaccttacctatctattaagttcatccgatcctaagaatatatctacttgtttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - caacaac
- - - - - - - - - - - - - -tgctgta
- - - - - - - - - - - - - - - - - - tgcttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgatcc