Sequence
atgc intronic sequence ATGC exonic sequencegtaaactgacaatctttgccagagtttcttttgaactggtgtatctgaaatattgatttaagcgtcgtgctacttgcttgcagTCTGCAATTGGGTCGGTTGCTGCTGCTGCAGAGCAAGCATTCAATCCATACGCTGAGAGGGTTCTAGAGTTGATGAAGTTTTTCATGGTGCTCACCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G27640.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G27640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G19960.1 (Glycine max), 3'ss of exon 7
-------------------------gtaaactgaca-atctttgccagagtttcttttgaactggtgtatctgaaatattgatttaagcgtcgtgctacttg--cttgcagTCTGCAATTGGGTCGGTTGCTGCTGCTGCAGAGCAAGCATTCAATCCATACGCTGAGAGGGTTCTAGAGTTGATGAAGTTTTTCATGGTGCTCACCAAAG
| | || || | | | || ||| || | | | | ||| | ||||| || || |||||||||||| ||||| || | ||| ||||||||||||||||||||| ||| || || || |||||| ||||||||||||| ||||||||||| | || || |
gtatggggaagatttagtatgctgtaaagattgtcacaattacaatgtatcagctattggtttgttatttttctaatttaaatttatattgtccactggatgtccttgcagTCTGCCATTGGTTCTATAGCTTCTGCTGCAGAGCAAGCATTCATTCCTTATGCCGAAAGGGTTTTAGAGTTGATGAAAATTTTCATGGTGTTAACTAATG
upper sequence: AT4G27640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G05090.1 (Glycine max), 3'ss of exon 7
------------------gtaaactgacaatctttgccagagtttcttttgaactggtg-tatctgaaatattgatttaa----gcgtcgtgct----acttgcttgcagTCTGCAATTGGGTCGGTTGCTGCTGCTGCAGAGCAAGCATTCAATCCATACGCTGAGAGGGTTCTAGAGTTGATGAAGTTTTTCATGGTGCTCACCAAAG
| | | || | | | | | | | || || | | | | | | |||||| | || || | | |||||||||||| ||||| || | ||| ||||||||||||||||||||| ||| || || || |||||| ||||||||||||| |||||||||| | || || |
gtatggggaagattttgtatggtgtaaagattgtcacaattgcaatgtatcagctattggtttgttatttttctatttaaatttatattgtcctctggatgtccttgcagTCTGCCATTGGTTCTATAGCTTCTGCTGCAGAGCAAGCATTCATTCCTTATGCCGAAAGGGTTTTAGAGTTGATGAAAAGTTTCATGGTGTTAACTAATG
upper sequence: AT4G27640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv12s0034g02160.t01 (Vitis vinifera), 3'ss of exon 7
-------------------gtaaactgacaatctttgccagagtttcttttgaa---ctggtgt-atctgaaatattgatttaagcgtcgtgctact-tgcttgcagTCTGCAATTGGGTCGGTTGCTGCTGCTGCAGAGCAAGCATTCAATCCATACGCTGAGAGGGTTCTAGAGTTGATGAAGTTTTTCATGGTGCTCACCAAAG
| | | || || | | | | ||| ||| || | | | || | | || ||||| | | ||||| | ||||||||||||||||| || ||||| |||||||||||||||||||| |||||| ||||| |||||||| ||||||||||| |||||||||||| ||||| |
gtataaagatatctttccttttctccaaaaacctctac-ataatttagtttaaatgtcaaatttgattttatttaccatgttaagatttctcctactgttattgcagTCTGCAATTGGTTCAGTTGCGGCTGCTGCAGAGCAAGCATTTGTTCCATATGCTGAAAGGGTTCTGGAGTTGATGAAAAATTTCATGGTGCTTACCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgaactggtgtatctgaaatattgatttaagcgtcgtgctacttgcttgcagTCTGCAATTGGGTCGGTTGCTGCTGCTGCAGAGCAAGCATTCAATCCATACGCTGAGAGGGTTCTAGAGTTGATGAAGTTTTTCATGGTGCTCACCAAAG
tattgat putative branch site (score: 3)
cttgctt putative PPT
tgaaatattgatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactgacaatctttgccagagtttcttttgaactggtgtatctgaaatattgatttaagcgtcgtgctacttgcttgcagTCTGCAATTGGGTCGGTTGCTGCTGCTGCAGAGCAAGCATTCAATCCATACGCTGAGAGGGTTCTAGAGTTGATGAAGTTTTTCATGGTGCTCACCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG