Sequence
atgc intronic sequence ATGC exonic sequencegtaaggactactatacctcaaagcctctttaaccatcatctaacatttttatgtttttgattaaatgctttggtgttctatttgcagATAAAGAACCTCCCGAAAGGGGCCACCGTTGTTGACTACGCTTATCTGATTCACACCGAAATCGGAAACAAGATGGTAGCAGCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02260.2 |
intron # | 17 |
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 17
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 17
gtaaggactactatacctcaaagcctctttaaccatcatctaacatttttatgtttttgattaaatgctttggtgttctatttgcagATAAAGAACCTCCCGAAAGGGGCCACCGTTGTTGACTACGCTTATCTGATTCACACCGAAATCGGAAACAAGATGGTAGCAGCAAAG
|| ||| | || || | | | | || | ||| | | || | || | || ||| | || ||| ||| |||||| || ||| | || || |||||||| || ||||| || ||||| ||||||||||| ||||| || ||||| |||||||| ||||||
gtgagg--tgctg-acttggaggacattt---cttccatttgag---ttgagcgattggtttgaata---tagttttc-attggcagATTAAAAACTTGCCTAAGGGGGCCACTGTGGTTGATTATGCTTACCTGATTCACACAGAAATTGGGAACAAAATGGTAGCTGCAAAG
upper sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 16
gtaaggactactatacctcaaagcctctttaaccatcatctaacatttttatgtttttgattaaatgctttggtgttctatttgcagATAAAGAACCTCCCGAAAGGGGCCACCGTTGTTGACTACGCTTATCTGATTCACACCGAAATCGGAAACAAGATGGTAGCAGCAAAG
|| ||| | | || | | | | || ||| | ||||| | | | | ||| | || || |||| || ||||| || || || ||||| || ||||| || |||||||||||||| || |||||||| ||||| ||| | |||||||||
gtgagg--caatgaactcagagatattagttaacagcatagactattttggaggctctaaataagc---------tgttacatgtagATTAAAAACCTGCCTAAGGGAGCCACGGTGGTTGATTATGCTTATCTGATTCATACTGAAATCGGCAACAAAATGATTGCAGCAAAG
upper sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 19
-----------------------------------------gtaaggactactatacctcaaagcctctttaaccatcatctaacatttttatgtttttgattaa--atgctttggtgttctatttgcagATAAAGAACCTCCCGAAAGGGGCCACCGTTGTTGACTACGCTTATCTGATTCACACCGAAATCGGAAACAAGATGGTAGCAGCAAAG
| | | | | | | | | | | || | | | || ||| || | || |||| ||| ||||||| ||||| || || | || || || || |||||||||||||| |||| ||||| ||||| || |||||||||||||| ||||||
gtaaggattggtctgtcatataccatgactattttttcccccttcagttgattgaagaagacaattttagaacatgtatttcaatactatc-tgccttttcttgatgattttttgtcacattatatgcagATTAAGAATCTTCCTCAGGGTGCTACTGTCATTGACTACGCTTATATGATACACACTGAAATAGGCAACAAGATGGTAGCTGCAAAG
upper sequence: AT4G02260.3 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 17
----------------------------------------gtaaggactactatacctcaaagcctctttaaccat-catctaacatttttatgtttttgatta--aatgctttggtgttctatttgcagATAAAGAACCTCCCGAAAGGGGCCACCGTTGTTGACTACGCTTATCTGATTCACACCGAAATCGGAAACAAGATGGTAGCAGCAAAG
| || | | | | | || ||| || | | | | || ||| || ||| |||| | | ||||||| ||||| || || | || || || || ||||||| |||||| |||| ||||| ||||| || |||||||||||||| ||||||
gtaaggattggtctgtcatataccatgcctatctttccccccttcaattaattgaagaagacaattttagaaacatgtatttgaatactatctgccttttcttgataattttttgtcacattttatgcagATTAAGAATCTTCCTCAGGGTGCTACTGTCATTGACTATGCTTATATGATACACACTGAAATAGGCAACAAGATGGTAGCTGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatcatctaacatttttatgtttttgattaaatgctttggtgttctatttgcagATAAAGAACCTCCCGAAAGGGGCCACCGTTGTTGACTACGCTTATCTGATTCACACCGAAATCGGAAACAAGATGGTAGCAGCAAAG
ttctattt CT-rich tract
atctaacatttttatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggactactatacctcaaagcctctttaaccatcatctaacatttttatgtttttgattaaatgctttggtgttctatttgcagATAAAGAACCTCCCGAAAGGGGCCACCGTTGTTGACTACGCTTATCTGATTCACACCGAAATCGGAAACAAGATGGTAGCAGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG