Sequence
atgc intronic sequence ATGC exonic sequencegtatgattcgactcgcggactctagaaaaatatatatgattgatacatcaacatgaaaaggtcttctaacagtgagtgtttgtgttaaagCTTTCTCGGAGCTATGATTCGGAATTCGGTGGGTTTGGATCTGCACCAAAGTTCCCGAGGCCTGTCGAGATCCAGCTGATGCTTTATCATTACAAAAAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G03200.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G03200.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G39560.1 (Glycine max), 3'ss of exon 7
-----------gtatg-attcgactcgcggactctagaaaaatatatatgattgatacatcaacatgaaaaggtcttctaacagtgagtgtttgtgttaaagCTTTCTCGGAGCTATGATTCGGAATTCGGTGGGTTTGGATCTGCACCAAAGTTCCCGAGGCCTGTCGAGATCCAGCTGATGCTTTATCATTACAAAAAGT
||| ||| | | | | | | |||| | | || | | ||| | || | | ||| || |||||||| ||||||||||||| | || ||||| |||||||||||||||||||| || || || || ||||| | ||||||| ||||| | ||||||||
aaattatatcgacatgtatttgttggatgttttgaatcgttaaaattatgctgagtgtttcgaatcttgagtgtcattcaat--ctactcttttctttgtagCTTTCTGGGAGCTATGATTCAAAGTTTGGTGGTTTTGGATCTGCACCAAAGTTTCCCAGACCAGTTGAGATAAACTTGATGCTATATCACTCCAAAAAGT
upper sequence: AT4G03200.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G36910.1 (Glycine max), 3'ss of exon 7
-----------gtatg-attcgactcgcggactctagaaaaatatatatgattgatacatcaacatgaaaaggtcttctaacagtgagtgtttgtgttaaagCTTTCTCGGAGCTATGATTCGGAATTCGGTGGGTTTGGATCTGCACCAAAGTTCCCGAGGCCTGTCGAGATCCAGCTGATGCTTTATCATTACAAAAAGT
| ||| ||| | | | | | | |||| | | | | || | | || | | ||| || |||| ||| ||||||| ||||| | || |||||||||||||||||||||||||| || || || || ||||| | ||||||| ||||| | ||||||||
atcttatatcagcatgtatttgttggatgttttgaatccttaaagttatgctgagtgttttgaatcttgaaaaccattcaat--ctactcttttctttgtagCTCTCTGGGAGCTACGATTCAAAGTTTGGTGGGTTTGGATCTGCACCAAAGTTTCCCAGACCAGTTGAGATAAACTTGATGCTATATCACTCCAAAAAGT
upper sequence: AT4G03200.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0104g01480.t01 (Vitis vinifera), 3'ss of exon 7
gtatgattcgactcgcgg---actctagaaaaatatatatgattgatacatcaacatgaaaag---gtcttct-aacagtgagt----gtttgtgttaaagCTTTCTCGGAGCTATGATTCGGAATTCGGTGGGTTTGGATCTGCACCAAAGTTCCCGAGGCCTGTCGAGATCCAGCTGATGCTTTATCATTACAAAAAGT
|| | |||| || ||| | ||| || || ||| || | | || |||||| || || | ||| | ||| |||| || ||| ||||||| | || | |||||||||||||||||||||||||| || ||||| || ||||| || || |||||||||||||| |||||||
gttgtcatggacttccgtttcactttttgttgata-atttggttgttaatgctttccgtaatttccatcttcttaattgtcctttttcatttctcttatagCTGGCTGGGAACTATGATCCTGAGTATGGTGGGTTTGGATCTGCACCAAAGTTTCCTAGGCCAGTTGAGATTCAACTAATGCTTTATCATTATAAAAAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgattgatacatcaacatgaaaaggtcttctaacagtgagtgtttgtgttaaagCTTTCTCGGAGCTATGATTCGGAATTCGGTGGGTTTGGATCTGCACCAAAGTTCCCGAGGCCTGTCGAGATCCAGCTGATGCTTTATCATTACAAAAAGT
ttctaac putative branch site (score: 1)
atgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattcgactcgcggactctagaaaaatatatatgattgatacatcaacatgaaaaggtcttctaacagtgagtgtttgtgttaaagCTTTCTCGGAGCTATGATTCGGAATTCGGTGGGTTTGGATCTGCACCAAAGTTCCCGAGGCCTGTCGAGATCCAGCTGATGCTTTATCATTACAAAAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT