Sequence
atgc intronic sequence ATGC exonic sequence...atgctgcatggctttccacctgctgatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
atgctgcatggctttccacctgctgatgtagcttttattgc-tgcttgtttc---tgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
|| | ||||| || | | | | | | |||| | | | || ||| | ||| || ||||| || ||||| || || | ||| ||||||||||| ||| | || ||||| |||||||||||||||||||||||||| | |||||||| |||
--tttggagagcttttgcattg--agtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
--------------------atgctgcatggctttccacctgct---gatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
||| ||| | |||| | ||||| || | || | || | | | | || | || || | | | | | |||| |||||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||||||||||||||| ||| | |||||||||||
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgta-tttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 8
-----------------------atgctgcatggctttccacctgctga-tgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
||||| | ||| || | | |||| | || || | || | | | || | || || | ||| ||| | || |||| |||||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||||||||||||||| ||| ||||||||||||
gtttggctgttttgagatttataatgctttctatttttttttctcttaaatgtatttggaatgtttgtccatatcc-tttagcatattagaatggtct-cttagaattttcataaatgacttagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCTTGATGGGAAGGAA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
------------------------------------------atgctgcatggctttccacctgctgatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgacaatcttcctggta----aacaca--------gGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
| || || ||| | || | | ||| || ||| | | | | | | ||| |||| || | | || | |||| | ||| |||||||| || |||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| ||||| ||||| ||||||||||||
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------------atgctgcatggctttccacctgctgatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
|| |||||| | | || | | | || || | | || | | | |||| | ||| | | | | | |||| |||||||| || |||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| ||||| ||| | ||||||||||||
gtttgactatgaagtttatgttgctttgtgtttattttattgtttctttatttttttaattatatatttgggcttttttttttcagacacatgtgatgtttctacatagtttttcacaataga----aattcttttcaaacattttgacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATCCTGATGGGAAGGAA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 8
atgctgcatggctttccacctgctgatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactga-caatcttcctggtaaac----acagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
|| | || | || || || || | | ||| | || | | | | | ||| ||| ||| |||| || || | |||| |||||||| || |||||||| ||||||||||| ||||| ||||| |||||||||||||| ||||||||||| || | |||||||| |||
---atgtaatgcctatggtagtcttttgccttttccatcatt-ttcatttttcactttttattttta-tcatcagttgatcaagcttcttgtcaatttataatagGTGTATACAGTTGGCCCTGAATATGCACATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGCGTTGTTATGAGAAACCCCGATGGGAAAGAA
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
atgctgcatggctttc-cacctgctgatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgaca--atcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
| | ||||| || || || | || | | | ||| | | | | | ||| | | ||| | | | | | | ||||| ||||||||||| || ||||| || ||||| ||||| |||||||| |||||||| |||||||| || ||||| | | | ||||| |||||
acatctgttagctttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaag---acgagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttctgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
aactgac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgctgcatggctttccacctgctgatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - -ctgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcaact