Sequence
atgc intronic sequence ATGC exonic sequencegtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G01250.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 3'ss of exon 6
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
| || | | || ||| ||| || | ||| | ||| | |||| || || || | | || ||||| | | || ||||||| ||||| |||| ||||||| | | || ||||| | || || || || ||||||||||| |||||||||||||| |||||||
-------gtttgccaccttgaa--tctcacttgttctgcttt-tactg-tgtcaa-ttggtaccttacagtcttggtgtttgta-----------tcagGGTTTGGGTAAGCATGACATCATCTGCATTGAGGATCTTGTTCATGAGATCATGACTGTTGGCCCACATTTCAAGGAGGCCAACAACTTCCTCTGGCCAT-------------------------------------------------------------------------------
upper sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 6
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaa--gactcacga-attcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
| ||| || ||| | | || | ||||| | || | | || |||||| | | | | |||||||| || ||| |||| ||||| | |||||| ||| ||||||| ||||| | || || |||||||| || ||||| || |||||||||||||||||||
-----------------------gtattgtttattttacaattcttccttacagattttaattaattcgctacatgcttcttacttgcttggatga---cagGCTCTGGGCAAGTATGGAATCATATCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGACCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT-------------------------------------------------------------------------------
upper sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
|| || || | | | || | || || | || | | | || ||||| || || |||| | | ||| ||| || | || |||||||| ||||||||| ||| ||| ||||||| ||||| | || || ||||||||||||||||| |||||||| || || ||||| |
gtctgt--ctggtgtaccggctagtcatctttaaatatctccattgct-tgtttgttctattactcagttttttcgctgacata-acattcaatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT-------------------------------------------------------------------------------
upper sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 6
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaa--gactcacga-attcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
| ||| | |||| || | | || || || || | |||| | || ||||| | | | | ||||| || || || |||| ||||||| |||||| ||| ||||||| ||||| | || || || ||||| || ||||| || |||||||||||||||||||
-----------------------gtattgttaatttacaatt-ctgtattacaaatttgaattaattcactacatgcttctgacttgcttggatga---cagGCGCTGGGCAAATATGGAATCATTTCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGGCCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT-------------------------------------------------------------------------------
upper sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 5
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
|||| | |||| ||||| ||||| || | || | | | | | | | | || || ||| | | ||||| | || ||| |||||| ||||||| || ||| | || || ||||| | || || ||||||||||| ||||| |||||||||||||| |||||||
gtttt---tatgtcattctgta--tcttggttttctatgagcgattgtttgctatatcttg---ttgctaac-ctgcttttgtgatga--------tagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT-------------------------------------------------------------------------------
upper sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
|| | | ||| ||| | || ||||| || | | | | | | | | | | || | | | | ||||| | || ||| |||||| ||||||| || ||| | || || ||||| | || || ||||||||||| ||||| |||||||||||||| |||||||
-----------gtttttatgtcattct--gtatcttggtttt---ctatgagcgattgtttgctttatct-tgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT-------------------------------------------------------------------------------
upper sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatc----aggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
| | | | || | | | ||||| | |||| | | | | || ||| || | | | |||| ||||||||| |||||||| || | ||||||| | || || ||||| | || || |||||||| |||||||||||||||||||| | ||| | |
tcgtataaatagctgcattgcgacacaattaaaattagtag-gacctgacgtgtatcctttg--cagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT------------------------------------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
ttctaac putative branch site (score: 1)
cctcatttc putative PPT
atttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG