Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatcagatcttttgttattcaggttatatcttatctacattgggactgaacatatgtcttacagGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGAGCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02260.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 14
gtatgtatcagat-cttttgttattcaggttatatcttatctacattgggactg---------aacatatgtcttacagGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGAGCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTC
|| | | | |||| ||||||| || | ||| || ||| || || | || |||| |||||||||||||||||||| ||||| ||||||||||| || || || || || ||||| ||||| || ||||||||||||| | |||| ||||
--gtgagttatctgctttccttattcattataatttttacctcttttgattttgccatttctaaaagccagctgtatagGTGAAAGATTACATTGCAACCCCAAAGCCTAATGGATACCAAAGTCTACACACGACAGTGATACCATTTCTGAATGAGAGTATGTTCCATTTGGAAGTTC
upper sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 16
---------------------------gtatgtatcagatcttttgttattcaggttatatcttatc-tacattgggactgaacatatgtcttac--------agGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGAGCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTC
| ||| | | || ||| | | ||| || || | | ||| ||| || || || |||| || ||||| ||||||||||| || || ||||| |||||||| || || || |||||||||||||| ||||||||||| |||||| | || || || |
gtacgtatgttattttctattatatttgagagtagaaagtgtta-gttttaagagacataaattttcattgactggtgtggaatatttggtttgttttgttttagGTGAAGGATTATATTGCAACCCCTAAACCAAATGGCTACCAGAGTCTTCAGACCACTGTGATTCCATTTTTGTATGAGAGCATGTTTAGGCTAGAAGTCC
upper sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 14
---------------------gtatgtatcag-----atcttttgttattcaggttatatcttatc-tacattgggactgaacatatgtcttac--------agGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGAGCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTC
||| | ||| | || ||| | | ||| || || | | ||| ||| || || || |||| || ||||| ||||||||||| || || ||||| |||||||| || || || || ||||||||||| ||||||||||| |||||| | || || || |
gtatgtatgctattttctattatatttgacagtagaaagtgttagttttaagagacataaattttcattgactggtgaggaatatttgatttgttttgttttagGTGAAGGATTATATTGCAACCCCTAAACCAAATGGCTACCAGAGTCTTCAGACCACCGTGATTCCATTTTTGTATGAGAGCATGTTTAGGCTAGAAGTCC
upper sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 14
------------------------------gtatgtatcagatcttt-tgttattcaggtta--tatcttatctacat-tgggactgaacatatgtcttacagGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGAGCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTC
| || || || | | | | || | || || |||| | | | | | | | | |||| | ||||| || |||||||| || || || ||||| || || || |||||||| ||||| |||||||| | |||||||| |||||||||||||| ||||
gtgtgtactttgctttgcacatcctttgaaatttgcttctaatttaagtatcagacaaaatgactagtttttctagaaataatattttatttttttgcaacagATGAAAGACTATATTGCAACTCCAAAACCTAATGGCTATCAAAGTCTCCATACAACTGTAATTCCATTTCTTTATGAGAGCATGTTTCGACTGGAAGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttattcaggttatatcttatctacattgggactgaacatatgtcttacagGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGAGCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTC
ttatatcttatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatcagatcttttgttattcaggttatatcttatctacattgggactgaacatatgtcttacagGTAAAAGATTACATTGCAACCCCGAAGCCCAATGGATACCAGAGCCTCCATACTACTGTGATTCCATTCTTGTATGAGAGTATGTTTCGACTGGAGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG