Sequence
atgc intronic sequence ATGC exonic sequencegtaagggcatcttttgaatgtttgatttcctttatcaaggtttaatttctgaaagaatgacccattacttgtattctagAATGAGCTTTCTGCAATATTGAGATTTGGAGCGGAAGAACTTTTTAAAGAGGATAAAAATGATGAAGAAAGCAAAAAGCGGCTGTTGAGTATGGATATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G13370.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 10
---------------gtaagggcatcttttgaa---tgtttgatttcctttatcaaggtttaatttctgaaagaatgacccattacttgtatt---ctagAATGAGCTTTCTGCAATATTGAGATTTGGAGCGGAAGAACTTTTTAAAGAGGATAAAAATGATGAAGAAAGCAAAAAGCGGCTGTTGAGTATGGATATTG
|| |||| | | || | | ||| | ||| || || ||| | ||| | ||||||| ||||| || ||||||||||||||||| ||||| | || ||||| ||||| | ||||||||| | ||| ||| ||| || ||||| ||||
aattaaaattctgagagaaatgcattaaatagaatctggcttgtcacctcacttgtattttctgttttgctcttctgatgtgagctatacattttgccagAATGAACTTTCAGCGATATTGAGATTTGGAGCAGAAGAGTTATTCAAAGAAGATAAGACTGATGAAGAGACCAAGAAGAAGCTTGAAAGCATGGACATTG
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 21
---------------------gtaagggcatcttttgaatgtttgatttcctttatcaaggtttaatttctgaaagaatgacccattacttgtattctagAATGAGCTTTCTGCAATATTGAGATTTGGAGCGGAAGAACTTTTTAAAGAGGATAAAAATGATGAAGAAAGCAAAAAGCGGCTGTTGAGTATGGATATTG
| | | | |||| || ||| | | | | | | |||| ||| | || | | || | |||||||||| |||||||| || |||| ||||| || || ||||||||||| || | |||||||||||||||||| || || ||||| ||||||||||| |
tgcattgaattgtttttgtttatgcagacttgttttttattttttttattttatttaattacacaattactgtacccatcatttgcttctgaaacgacagAATGAGCTGTCTGCAATCTTACGATTCGGAGCAGAGGAGCTTTTTAAAGAAGAAAGAAATGATGAAGAAAGCAAGAAACGACTGTTAAGTATGGATATAG
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 21
-----------------------------------------------------------------------------------------gtaagggcatcttttgaatgtttgatttcctttatcaaggttta--atttctgaaagaatgacccattacttgtattctagAATGAGCTTTCTGCAATATTGAGATTTGGAGCGGAAGAACTTTTTAAAGAGGATAAAAATGATGAAGAAAGCAAAAAGCGGCTGTTGAGTATGGATATTG
| | | | ||| | ||| |||| | ||| | | | ||| ||| | ||| | | || || |||||||||| |||||||| || |||||||||| || || || ||||| || || | |||||||||||||||||| || | || || |||||| |||| |
gtaaggacatttgtgaaaactgtaatttcatgtgaatattcattaccttgctttcatcatttatggactgcattgaattgttttagtttatgcagacttggtttcttttttttattttttatatttaattacacaattactgtaccaatcatttgcttctgaaatgacagAATGAGCTGTCTGCAATCTTACGATTTGGAGCAGAGGAGCTCTTTAAGGAAGAAAGAAATGATGAAGAAAGCAAGAAACAACTCTTAAGTATGAATATAG
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 21
------------------gtaagggcatcttttgaatgtttgatttcctttatc--aaggtttaatttctgaaag-aatgacccattacttgtattctagAATGAGCTTTCTGCAATATTGAGATTTGGAGCGGAAGAACTTTTTAAAGAGGATAAAAATGATGAAGAAAGCAAAAAGCGGCTGTTGAGTATGGATATTG
| || | | ||| || || ||| || | | || | ||| || | || || | ||| |||||||||| || || || || || ||||| ||||| ||||||||||| || || |||||||| ||||||||||||||| |||| || |||||||||||||
tcctatgtcattttatatttttaggaacatgttgcattgctgttttttttggttgtatagtgtgattgctccatccaacattttcttttcttgattgcagAATGAGCTGTCGGCTATTTTAAGGTTTGGGGCGGAGGAACTTTTTAAGGAAGACAAAAATGAAGAAGAAAGCAAAAAGAGGCTCTTAAGTATGGATATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcctttatcaaggtttaatttctgaaagaatgacccattacttgtattctagAATGAGCTTTCTGCAATATTGAGATTTGGAGCGGAAGAACTTTTTAAAGAGGATAAAAATGATGAAGAAAGCAAAAAGCGGCTGTTGAGTATGGATATTG
gtttaat putative branch site (score: 4)
tttaatttctgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggcatcttttgaatgtttgatttcctttatcaaggtttaatttctgaaagaatgacccattacttgtattctagAATGAGCTTTCTGCAATATTGAGATTTGGAGCGGAAGAACTTTTTAAAGAGGATAAAAATGATGAAGAAAGCAAAAAGCGGCTGTTGAGTATGGATATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT