Sequence
atgc intronic sequence ATGC exonic sequencegtaatctctcaaaatttcactactgctttagaatctgaaactggatctgaaattgtagcttcttatttaatggtggattctctttgattaatgcagTGTGAGTGTGTTTGGTGTATCGGCGGAATCGATGCAATGTTCTTATGATGAGAAAGGAAACAGTGTCCCAACGATTCTATTACTTATGCAGGAGAGACTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G03100.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 1
gtaatctctcaa-aatttcactactgctttagaatctgaaactggatctgaaattgtagcttcttatttaatggtggattctctttg---attaatgcagTGTGAGTGTGTTTGGTGTATCGGCGGAATCGATGCAATGTTCTTATGATGAGAAAGGAAACAGTGTCCCAACGATTCTATTACTTATGCAGGAGAGACTC
|| ||| | | ||| | || ||||| | | | ||||||| || | || | | ||| |||| | || |||||||| |||||||||||||| || || ||||| ||||| |||||||||||| ||||||||||||||||| || ||||| || || |||||||| | ||
ttattcttctagcagttttttttcttctttatttttgttgtcctttgccatgtttgtagcatcgttttaacttgtgatttcttgtcatgtatgcttgcagTGTAAGTGTGTTTGGTGTCTCAGCAGAATCTATGCAGTGTTCTTATGATCCAAAAGGAAACAGTGTCCCCACTATTCTTTTGCTAATGCAGGACCGTCTA
upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 1
gtaatctctcaaaatttcacta--ctgctttagaatctgaaactggatctgaaattgtagcttcttatttaatggtggattc---tctttgattaatgcagTGTGAGTGTGTTTGGTGTATCGGCGGAATCGATGCAATGTTCTTATGATGAGAAAGGAAACAGTGTCCCAACGATTCTATTACTTATGCAGGAGAGACTC
|| | | || | | | ||| ||| || | ||||||| || | || | | | | ||| || | || |||||||| || |||||||| || || || ||||| ||||| |||||||||||| ||||||||||||||||| || ||||| || || |||||||| | ||
-ctgacttttattcttctagcaggttttttttttgtctttgtcttttcccatgtttgtagcatcgttttaacttgcgatttcttgtcctgtatgcttgcagTGTAAGCGTGTTTGGGGTCTCAGCAGAATCTATGCAGTGTTCTTATGATCCAAAAGGAAACAGTGTCCCCACTATTCTCTTGCTAATGCAGGACCGTCTA
upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G39280.1 (Glycine max), 3'ss of exon 1
--gtaatctctcaaaatttcactactgcttta---gaatctgaaactggatctgaaattgtagcttcttatttaatggtggattctctttgattaat-gcagTGTGAGTGTGTTTGGTGTATCGGCGGAATCGATGCAATGTTCTTATGATGAGAAAGGAAACAGTGTCCCAACGATTCTATTACTTATGCAGGAGAGACTC
| ||| || || | | | || | || | | | | ||| | ||| | ||| | ||| || | | || ||| ||||||| ||||||||||| || || || ||||| ||||| ||||| |||||| ||||||||||||||||| || |||||| | || ||||| ||| || |
tagaaatttcatcgaactatgtacttattctatctgtatttaccatttcttatgagttatgagc--catatgctaatgtgattttcccatcatcaattgcagTGTTAGTGTGTTTGGCGTCTCAGCAGAATCAATGCAGTGTTCCTATGATTCAAAAGGAAACAGTGTCCCCACTATTCTACTGCTAATGCAAGAGCGATTA
upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G36630.1 (Glycine max), 3'ss of exon 1
gtaatctctcaaaatttcactactgctttagaatctgaaactggatct---gaaattgtagcttcttattta-atggtg----gattctctttgattaat-gcagTGTGAGTGTGTTTGGTGTATCGGCGGAATCGATGCAATGTTCTTATGATGAGAAAGGAAACAGTGTCCCAACGATTCTATTACTTATGCAGGAGAGACTC
| | |||| | ||| || |||| |||| | ||| || | | || | ||| | |||| ||| | || ||| ||||||| ||||||||||| || || || ||||| ||||| ||||| |||||| ||||||||||| ||||| || |||||| | || ||||| || || |
----tgggtttggggttca-tgtattttttctttcctaaacctcatctagcaagattatatatcttcatccatatgctaatctgattttctatcatcaattgcagTGTTAGTGTGTTTGGCGTCTCAGCAGAATCAATGCAGTGTTCCTATGATTCAAAAGGAAACAGCGTCCCCACTATTCTACTGCTAATGCAAGATCGATTA
upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 1
gtaatctct-caaaatttcactactgctttagaatctgaaactggatctgaaattgtagcttcttatttaatggtggattctc---tttgattaat---gcagTGTGAGTGTGTTTGGTGTATCGGCGGAATCGATGCAATGTTCTTATGATGAGAAAGGAAACAGTGTCCCAACGATTCTATTACTTATGCAGGAGAGACTC
|| ||| | |||| |||| | | ||| ||||| | || | || | || | | | | ||| |||| | |||| ||||||||||| || || |||||||| |||||||||||||||||| |||||||| || ||||| || ||||| || || ||||||||||| |
-tagattctactgaattccact-ttattcctatctctcct-ttggattcaattttctgaattttggttgagataccaacttttgtgtttatgtaattttgtagTGCAAGTGTGTTTGGCGTCTCTGCGGAATCAATGCAATGTTCTTATGATTCAAAAGGAAATAGCGTCCCCACTATTCTCTTGCTAATGCAGGAGAGGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatctgaaattgtagcttcttatttaatggtggattctctttgattaatgcagTGTGAGTGTGTTTGGTGTATCGGCGGAATCGATGCAATGTTCTTATGATGAGAAAGGAAACAGTGTCCCAACGATTCTATTACTTATGCAGGAGAGACTC
gattaat putative branch site (score: 3)
ttcttatttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctctcaaaatttcactactgctttagaatctgaaactggatctgaaattgtagcttcttatttaatggtggattctctttgattaatgcagTGTGAGTGTGTTTGGTGTATCGGCGGAATCGATGCAATGTTCTTATGATGAGAAAGGAAACAGTGTCCCAACGATTCTATTACTTATGCAGGAGAGACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA