Sequence
atgc intronic sequence ATGC exonic sequencegtcggtagtcacgtctcatgataactttgccaatgaacttattgattcataaagcatgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03940.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
-------------------------------------------------------gtcggtagtc---acgtctcatgataactttgccaatgaact------tattgattcataaagcatgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
| | || | || |||| |||| || | | || || | || | | | || | | | | | |||||| ||||| |||| || || ||||| || || || ||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||| ||| |
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggcttagttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
gtcggtagtcacgtctcatgat---aactttgccaatgaacttattgattcataaagcatgaaagccgttttacttattccacttcatgtaat-gcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
|| ||| | || || || ||| || ||| ||| | | || | | | | | | || | | | | || | ||||||||| || || ||||| || ||||||||||| || || ||||| | ||||||||| || |||||||||||||||||||| ||||| ||||| ||| |
ttctactctcaactgtctggactccaatttttcctgtgagcttctggtgtccttccat-tagatactatcgttctaaaccaggcatgtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 14
gtcggtagtcacgtctcatgataactttgccaatgaacttattgattcataaagcatgaaagccgttttacttattccacttcatgtaatgcgat----agGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
|| || | || | |||| | | | | || || || | |||| | | | | || | || | | | |||||||||||| || || || ||||||||||| || || || ||||| ||||| ||||| || || || ||||||||||| |||||||| ||||| |||||
gtatatattgac-ttgcatgttccacacacttagtgtttcttttgtttatgtattatgacatgaatggggttagtctgacatggtgatttactctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCAAATGGATCAACAAGAAATGGAAAGAAGGATTTCATGTTACATCAATGAC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 10
gtcggtagtcacgtctcatgataa-ctttgccaatgaacttattgattcataaagc-----atgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
||| | || || ||| | | | | ||| | | | || ||| || ||| || | | ||| | ||| |||||||||||| ||||||||||| ||||| || || || || ||||| | ||||||||| ||||| |||||||||||||| || ||||| ||||||||| |
gtcataatgcaatctctattttaagcctcgttgcatcgcgcattaactatcagggcctacgatggtagtaatttggggtaatatatttc---cactgctgcagGAACTCCTTACACCCAGCAATCATACAAGGTTAGTGAGTCGTTTCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
-gtcggtagtcacgtctcatgataa-ctttgccaatga-acttattgattcataaagcatgaaagccgttttacttattccacttcatgt--aatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
||| || || | ||| ||| | | || ||| ||| | | || | | | | || | | || | | | | |||||||||||| || |||||||| ||||| || ||||| || || || | ||||||||| |||||||||||||||||||| || ||||||||||| ||| |
tgtcc-tatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgcta-tgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 9
gtcggtagtcacgtctcatgataa-ctttgccaatgaacttattgattcataaagc-----atgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
||| | || || ||| | | | ||| | | | || ||| || ||| || | | ||| | ||| |||||||||||| ||||||||||| ||||| || || || || ||||| | ||||||||| ||||| |||||||||||||| || ||||| ||||||||| |
gtcataatgcaatctctattttaagccccgttgcatcgcgcattaactatcagggcctgcgatggtagtaatttggggtaatatatttc---cactgctgcagGAACTCCTTACACCCAGCAATCATACAAGGTTAGTGAGTCGTTTCCTTACAAGTGGATTAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 14
-gtcggtagtcacgtctcatgataactttgccaatgaacttattgattcataaagcatgaaagccgttttactt----attccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
|| | | | ||| | || | || || || | | | | || |||| | ||| || | | | |||||||||||| || ||||| ||||||||||| || || ||||| || | ||||||||| || || || |||||||||||||||||||| ||||| |||||
tttctgcgattctatag-atgtttggcctgtctctgtaccctttcactt-tgccttgtctgcatcgatttatctgtgcattaaacctttttactttttgcagGAACTCCTTACACTCAGCAGTCTTACAAAGTTAGTGAATCATTCCCCTACAAGTGGATCAACAAGAAATGGAAAGAAGGTTTTCATGTTACATCAATGAC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 14
gtcggtagtcacgtctcatgataa-ctttgccaatgaacttattgattcataaagc-----atgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
||| | || || ||| | || || ||| | | | || ||| || ||| || | | ||| | ||| |||||||||||| ||||| ||||| ||||| || ||||| || || || | ||||||||| ||||| |||||||||||||| || ||||| ||||||||| |
gtcataatgcaatctctattttaagccctgttgcgtcgctcattaactatcagggcctgcgatggtagtaatttggggtaatatatttc---cactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 14
gtcggtagtcacgtctcatgataactttgccaatgaacttattgattcataaagcatgaaagccgttttacttattccacttca-----tgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
| | | ||| | | || | | | | ||| | | || | | | || || |||| || | | | |||||||||||||| || ||||| || |||||||| || || |||||||| ||||| |||||||| || |||||||||||||| || ||||| || || |||||
-tattttagctcgtttaacttctgtgatgaaaggaacatcaactgttcttcaga-atttatgactttatatttatctcatgtttgaatcctttactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCAAATGGATAAACAAGAAGTGGAAAGAAGGATTCCATGTTACCTCAATGAC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
gtcggtagtcacgtctcatgataactttgccaatgaa-cttat--tgattcataaagcatgaaa---gccgttttacttattccacttcatgtaat-gcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
|||| | || | | | || | | || ||| | || | |||| | | | ||| | | |||| | | | | | |||||||||||||||||||||| || |||||||| || || || ||||| || || ||||| ||||| ||||||||||||||||| ||||| ||||| |||||
----tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------------------------------------gtcggtagtcacgtctcatgataactttgccaatgaacttattga---ttcataaagcatgaaagccgttttactta---ttccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
| | | | ||| || || | || ||| ||| || | | || | | || | | | ||| | || | | ||||||| | || || ||||| ||||||||||| |||||||| |||||||| |||||||| ||||| || ||| |||||| ||| | || || || ||| |
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gtcggtagtcacgtctcatgataactttgccaatgaacttattgattcataaagcatgaaagccgttttacttatt-ccacttcatgtaatgcg-atagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
||||| || ||| ||| | || | | | ||| | ||| || || || || || ||||| |||||||| ||||| |||||||| ||||||||||| || |||||||||| ||||| ||| | || || |||||| |
--------------------------------------gtattg--tcgctgttattgatggccactggcattgtcgctgacgcgtgtttcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gtcggtagtcacgtctcatgataactttgccaatgaacttattgattcataaagcatgaaagccgttttacttatt-ccacttcatg-taatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
||||| || ||| ||| | || || | | || | | ||| || || || || || ||||| |||||||| ||||| |||||||| ||||||||||| || |||||||||| ||||| ||| | || || |||||| |
--------------------------------------gtattg--tcgctgttattgatggccactggcattgttgctgacgcgtgattcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattcataaagcatgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
tattgat putative branch site (score: 3)
ttttacttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggtagtcacgtctcatgataactttgccaatgaacttattgattcataaagcatgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG