Sequence
atgc intronic sequence ATGC exonic sequencegtcttttactttgcttctccaccttccttctctactctagctatcttcttcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61250.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G07960.1 (Glycine max), 3'ss of exon 2
-------gtcttttactttgcttctc-caccttccttctctactctagctatcttcttcttcattgtctga----attctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
| || | | || | | ||| || || || || |||| ||| | | ||| | || | | | | ||||||||||||||| || | ||||| ||||||||||||||||| ||||||||||||||||||||||| || || ||||||||||| | | ||||| ||
tcatgtagatattaataaagattataatagtttcagactatataataattactctctttttcttattttgacaatactcaacaaatgaacaaattcacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATCAAGAACTTATGGAACACCCACTTAAAGAAACGTCTCATTTGCATGGGCCTG
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G01540.1 (Glycine max), 3'ss of exon 2
---------------gtcttttactttgcttctccaccttccttctctactcta--gctatcttcttcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
| | | | | | || | | || || ||||| | || || ||| || | || | ||||||||||||||| || | ||||| ||||||||||||||||| ||||| || |||||||||||||| || |||||||||||||| | | ||||| |||
catgtcatgtagagattagtagaaaccatataatgatttctctctttttctttaaggctatatattttgacagtgttcaaaa---aaatgaaccaatt--cacagGTGGGCTGCTATAGCCTCTCAGCTACCAGGAAGAACAGACAATGAGATAAAAAACTTATGGAACACCCACTTGAAGAAACGTCTCATTTGCATGGGCCTT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 2
-------gtcttttactttgcttctccaccttccttc--tctactctagct-atcttct---tcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
| | |||| |||| || | | || || | | || || | | |||| | ||| | || | |||||||||||||| || || | ||| | ||||| ||||||||||| ||||| ||||||||||||||||| || |||||||| ||||| | ||||| |||
tacataaaattgctggtttgtttctttgaattacctgaatcagttcaaattcatattttaaatgcacatt-tatgactatatacattgaacaaattctcagGTGGGCTGCAATAGCCTCTCAGTTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAACACCCACTTGAAGAAGCGTCTCAAAAGCATGGGGCTT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G39720.1 (Glycine max), 3'ss of exon 2
-----gtcttttactttgcttctccaccttccttctctactctagctatcttcttcttcattgtctgaattctgcttttttttgttt-------cctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
| ||| | | | || |||| ||| | | | | | | | | || | | | ||||||||||||| || || | || | ||||| ||||||||||| ||||| |||||||||||||| ||||| |||||||| ||||| | |||||||||
tgttaacatagtacgtaaaaatttctggtttgttctttacctgaatcagttcagattcttattttaaaggcatatttatgactagataaacaaatttcagGTGGGCTGCAATAGCCTCTCAATTACCAGGGAGAACAGACAATGAGATAAAGAACTTATGGAATACTCACTTGAAGAAGCGTCTCAAAAGAATGGGTCTT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0046g03190.t01 (Vitis vinifera), 3'ss of exon 2
----------gtcttttac--tttgcttctcc-accttccttctctactctagctatcttcttcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
|| || | | |||| ||| || || | || | | ||| | | | | | || | ||| | | | ||||||||||||| ||||| | || || || ||||| || || || |||||||||||| |||||||||| || |||||||| || || | ||||| |||
ctttggttaggttttctgcaatttgtcactctgacattgatggaatattttca-tatttcatgttatgaacttttaacaatacttgatacactatgttcagGTGGGCTGCCATTGCCTCTCAACTGCCCGGAAGGACCGATAATGAGATCAAGAACCTATGGAACACCCACTTGAAGAAGCGCCTGCTTGGAATGGGGCTT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------gtct--tttactt-tgcttctccaccttccttctctactctagctatcttcttcttcat--tgtctgaattc------------tgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
|| | |||| ||| | | | | | | ||| | ||||| | | | | ||| | | | ||||||| ||| | || ||| | || || || | || || || |||||||||||||||| || || | |||||||| |||||||||||||| | | | ||| |
gtataaagcattttcgaagaattgagtttagcttacccatgccccgcaaatgtggcacatttctcagtacactttctttctgaaaatatttgattccgaaagcattgcacgttttttttggttggattagATGGTCAGCAATCGCGGGCCACCTGCCCCAGCGAACAGACAACGAGATAAAAAATTATTGGAACACGCATTTGAAGAAACGCTTGGCACACAGGGGAATC
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtcttttactttgcttctccaccttccttctctactctagctatcttcttc-------------ttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
| |||| |||| || | || || | | | | | || ||| | || | | || | || || || | ||| ||| |||| || || || ||||| | | || ||||||||||||||||||| |||||||| || |||||||| ||||| | ||||| ||
tttgttttgttttgtttttttgtgtttttttgtgtgtgtgtgcgagtgcgtggagcacagaaaaattgattttttggaatgtgttgttgttgatt--cgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATT
upper sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S106_216V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------gtcttttactttgcttctccaccttccttctctactcta-gctatcttcttcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
| | | | || | | | || ||| || | | || | | | | | ||| | ||| || || | | || ||| | || || || | || || || | |||||||||||||| ||||||| |||||||| ||||||||||||||| | | ||||| |
gtactgaattttcttcccgtcgcgttgggatgtctcatttctgcagacgtcgcgcgttggttacactccacaaaattgtcagttcctaacagcatttctcgtttcttgattgcattagATGGTCAGCCATCGCGGGCCATCTCCCCCAGCGTACAGACAACGAGATAAAGAACTACTGGAACACGCATTTGAAGAAACGTTTGGCACAGATGGGAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actctagctatcttcttcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
ttctgcttttttttgt CT-rich tract
ttttttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttttactttgcttctccaccttccttctctactctagctatcttcttcttcattgtctgaattctgcttttttttgtttcctcagGTGGGCTGCTATTGCAGCACAGCTTCCAGGAAGAACAGACAACGAGATCAAGAACTTATGGAACACTCATTTGAAGAAACGTCTTTTATCTATGGGTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA