Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcagttcattaacatttatacatgtgaaatacaaaactaacatttcttcaagactttgacttactttttttaatcatgttatggtttttgacagATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13890.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g51260.1 (Oryza sativa), 3'ss of exon 2
gtttgtcagttcattaacatttatacatgtgaaatacaaaactaacatttcttcaagactttgacttactttttttaatcatgttatggtttttgac------------agATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT-
|| || | | | | |||| | || | || ||| || || || | ||| | || || || || |||||||| ||||| || || |||||||| |||||||| || ||||||||||| ||||||||||| | ||| || ||||||||||| || || | |
---------ttgatctgagacaaaggacgggg--cgcaaatgtggcaatcgatcgagatttgagctggctaacatatgctgtgtcactgtgattcactgcattgcatgcagGTGGGCTCAGATTGCCAAGCACCTACCTGGTAGAACAGACAATGAGGTCAAGAACTTCTGGAACTCCACCATCAAGAAGAAGCTCATCTCCCAG-GCCGTG
upper sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G088783_T01 (Zea mays), 3'ss of exon 2
-gtttgtcagttcattaacatttatacatgtgaaatacaaaactaacatttct---tcaagactttgacttactttttttaatcatgttatggtttttgacagATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT-
| |||| | | |||| | | || ||||| || | | | | | || || | | || | | |||| ||||| || || || || ||||| ||||| ||||| || |||||||| ||||| ||||||||||| | ||| || ||||||||||| || || | |
catatgtcgccttaataacttgcttgggagtttgggacaaaggaaagagacgcgaatggaaaatgcagctagctaaaaatg--cgtgccactgcacac-acagGTGGGCCCAGATCGCCAAGCATCTGCCTGGTAGAACGGACAACGAGGTGAAGAACTTCTGGAACTCCACCATCAAGAAGAAGCTCATCTCCCAG-GCCGTG
upper sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 2
-----------------gtttgtcagttcattaacatt---tatacatgtgaaatacaaaact--aacatttct----tcaagactttgacttact--ttttttaatcatgttatggtttttgacagATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT
||| | | || ||| || | | | ||||| | | | | ||| |||| | | | | | || || | | || | || |||| |||||||| || || || || |||||||||||||||||||| ||||| ||||| || ||||| || ||||| || |||||||| | ||||| || |
gttttctttatctttttttttataaatttatttttcttatatttccccgtgaattgctctttttgatcatgatcaaagtcaacattattatcaaaaggttggtttgttaactttttcttaacaacagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAGAACTTTTGGAATTCAAGCATAAAGAAGAAGCTGCTTTCTCATGATGTT
upper sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G20440.1 (Glycine max), 3'ss of exon 2
----------------------------------gtttgtcagttcattaacatttatacatgtgaaatacaaaactaacatttcttcaagac--tttgacttactttttt--taatcatgttatggtttttg---acagATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT
||| || | || | ||| |||||| | | || | ||| ||| ||| | ||||||||| || | || |||||| ||||||||||||| || || || || |||||||||||||||||||| ||||| || || || ||||| || ||||| || ||||| ||| | ||||
gtataaccattgctatagccacacatgctcctttctttttctacttttttttttctattcatgtgcatcatcaa--cattattatcaaaaggttgttttatctacttttttctcaacaagagtaaactttttgggtacagATGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAAAACTTTTGGAATTCAAGCATAAAGAAGAAACTCCTTTCTC--------
upper sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G01050.1 (Glycine max), 3'ss of exon 2
--------------------------------gtttgtcagttcattaacatt-tatacatgtgaaata-caaaactaacatttct-tcaagactttgacttac------tttttttaatcatgttatggtttttg---acagATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT
|| | ||| || || ||| |||||| | | || | |||||| | |||| | |||| ||| |||| | || | || ||||| |||| |||||||| || || || || |||||||||||||||||||| ||||| || || || ||||| || ||||| || ||||| || | ||||| || |
gtataaccattgctagccacattccccttctttttctacttttcttttttgttctattcatgtgcatcatcatcatcaacattattatcaaaagtttgctttatctacttttttctcaacaagagtaaacttttttggtacagGTGGGCTCAGATAGCCAAGCACCTACCTGGAAGAACAGATAATGAGGTGAAAAACTTTTGGAATTCAAGCATAAAGAAGAAACTGCTTTCTCATGATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatttcttcaagactttgacttactttttttaatcatgttatggtttttgacagATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT
ttttt CT-rich tract
ttactttttttaatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcagttcattaacatttatacatgtgaaatacaaaactaacatttcttcaagactttgacttactttttttaatcatgttatggtttttgacagATGGGCTCAAATTGCTAAACATCTACCTGGAAGAACAGATAACGAGGTCAAGAATTTCTGGAACTCGAGCATTAAAAAGAAGCTCATGTCTCACCATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA