Sequence
atgc intronic sequence ATGC exonic sequencegtatatatatagataccctctcttctttcagttatcaggctcatattgtttctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34500.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G01490.1 (Glycine max), 3'ss of exon 4
------------gtatatatatagataccctctcttctttcagttatcaggctcatattgtttctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
| | | | | | || | |||| || | | | || | | | || | || || || ||||||||||||||||||||| || |||||||| ||||||||||| |||||| | || ||||| || ||||| || |||| || |||||| | ||||||||||||||
gttagttctttctcaagtcttggagttattttttcatttcctcttatatggaggtgaataatactatttacct-atatgatttcataccacaaattttctgcagATATGTTTCACCTGAGTATGCAAGCACTGGTATGCTTAATGAGGGAAGCGATGTGTATAGTTTTGGGATTCTACTGATGGAGCTAATTACAGGAAGGAGT
upper sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G01440.1 (Glycine max), 3'ss of exon 4
-------------gtatatatatagataccctctc--ttctttcagtt-atcaggctcatattgtttctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
| | || || | || |||| | ||| | | | ||| | ||| || || | || || | || || ||||||||||||||||||||| || |||||||| ||||||||||| |||||| | || ||||| || ||||| || |||| || |||||| | ||||||||||||||
gtttgttctttctcaagtcttggagttattttttcatttctcttagtggaagtgaataatactatttacctatatgatttcatcgttcataccacaaa-tttctgcagATATGTTTCACCTGAGTATGCAAGCACTGGTATGCTTAATGAGGGAAGCGATGTGTATAGTTTTGGGATTCTACTGATGGAGTTAATTACAGGAAGGAGT
upper sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G04780.1 (Glycine max), 3'ss of exon 4
gtatatatatagataccctct--cttctttcagttatcaggctcatattgtttctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
||| || | | | | | | | | | || ||| | || ||| | | | ||| | || | | || | || |||||||||||||||| |||| || |||||||| | |||||||| |||||| | |||||||| || || || || ||||| ||||||||||| || |||||||| |||
gta-atttgttctttctcaaggatctatgttacttttcaagttc-tatagatgataatcatctcatgatttctttccgct--aattttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
upper sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 4
-------gtatatatatagataccctctcttctttcagttatcaggctcatattgtt--tctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
|| | | || | | | || ||| || ||| | | | ||| || | ||| ||| || ||| ||||||||||| ||| |||| || |||||||| | |||||||| |||||| | |||||||| || || || || ||||| ||||||||||| || |||||||| |||
gtaatttgttctttctcaagtatctatgtcattactacttttcatcttc-tatggatgataattatcttctgatttcctaccactattt----ttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
upper sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0063g02510.t01 (Vitis vinifera), 3'ss of exon 4
----------------gtatatatatagataccctctcttctttcagtta---tcaggctca----tattgtttctttaca------ttttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
| |||| | | | | | | ||||| | | || |||| ||||| | | | |||| ||| | | | |||||| |||||||| || || || |||||||| || |||||||| | ||| | ||||||||||| ||||| || ||||| || |||||||| ||||| |||||||||
gtatgttcttcctcggtttcctataatatttttcaataatttgttagttagatttaaacttgaatgtattatttctctgtacacatgtattattaagttatttatcatcatttttctgtagATATGTCTCTCCCGAGTATGCAAGCACGGGTATGCTTAGTGAAGGGAGTGATGTCTATAGTTTTGGAGTTCTACTTATGGAGATAATTACTGGAAGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctcatattgtttctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
ttttaac putative branch site (score: 2)
cctttttaactttct CT-rich tract
atattgtttctttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatatagataccctctcttctttcagttatcaggctcatattgtttctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG