Sequence
atgc intronic sequence ATGC exonic sequence...caaattgaattcttggactaattttatcagcgttttttactacatgataatcgggatgctaatattattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTGCCTGGAATTTCAGATATGATTGAT
Basic information
species | Glycine max |
transcript | GLYMA09G40290.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G60950.1 (Arabidopsis thaliana), 3'ss of exon 6
-caaattgaattcttgga----ctaattttatcagcgttttttactacatgataatcgggatgctaatattattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTGCCTGGAATTTCAGATATGATTGAT
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gtacacttgctctgtaaagggtccagaataagatgcatttttgttattatcatt-ttatatctcctgtcttacaatgaccaactatttaaatgttctc-aaccagCCAAAACCAAGAATTGATTACACTCTGAAGGCTGTCCGTGGAAGCTTAACAGCAATTCCTGGACTATCTGCTATGATTGAT
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G61050.1 (Arabidopsis thaliana), 3'ss of exon 7
---caaattgaattcttggactaattttatcagcgttttttactacatgataatcgggatgctaatattattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTGCCTGGAATTTCAGATATGATTGAT
|| || | | | || | ||||| || || || | | | ||| | || ||| ||| | | | || || |||||||| || ||||||||||||||| ||||||||||||||||||| || || ||| | |||||| | || ||||||||||||
gtacacttttcctgtaaaggtccagaataagattcatttttcttatatcatt-ttatatctcctgtcttacaatgaccaactatttaaatgatctc-aaccagCCAAAACCAAGAATTGATTACACTCTGAAGGCTGTTGGTGGAAGCTTAACAGCAATTCCTGGACTATCTGATATGATTGAT
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G61030.1 (Arabidopsis thaliana), 3'ss of exon 6
-----caaattgaattcttggactaattttatcagcgttttttactacatgataatcgggatgctaatattattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTGCCTGGAATTTCAGATATGATTGAT
| || | || | | | | || ||||| || || | | | ||| | || ||| ||| | | || || |||||||| || ||||||||||||||| |||||||||| ||||||| || || ||| | |||||| | || | ||||||||||
gtacacttgttctgtaaagggtccagaataagatgcatttttgttattatcatt-ttatatctcctgtcttacaatgaccaactatttaaatgttctc-aaccagCCAAAACCAAGAATTGATTACACTCTGAAGGCTGTCCGTGGAAGCTTAACAGCAATTCCTGGACTATCTGCTATGATTGAT
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0048g01410.t01 (Vitis vinifera), 3'ss of exon 7
caaattgaattcttggactaattt-tatcagcgttttttactacatgataatcgggatgctaata-ttattttc--actgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTGCCTGGAATTTCAGATATGATTGAT
|| | | | || | | || |||| || | | | | | | | | | || |||| | ||||| | | | |||||||||||||| ||||||||||| ||| |||||||||||||||||||||| || || || ||||||||||||||||||||||||
----ttccagtatatcacaagctagtagatctattttgtaattgttaacactttaattaattacagttgttttggaattgactaatactcgtttgttcaatcagCCAAAGCCAAGAATTGATTATACTCTGAAGGCTGTTGGTGGAAGTTTAACAGCTCTCCCTGGAATTTCAGATATGATTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataatcgggatgctaatattattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTGCCTGGAATTTCAGATATGATTGAT
cattaac putative branch site (score: 2)
atgctaatattatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaattgaattcttggactaattttatcagcgttttttactacatgataatcgggatgctaatattattttcactgactttttcattaacatctaatcagCCAAAGCCTAGAATTGATTACACTTTGAAGGCTGTTGGTGGAAGTTTGACGGCACTGCCTGGAATTTCAGATATGATTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - -cttggac
- - - - - - - - - - - - - - - - - - - - tacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgct