Sequence
atgc intronic sequence ATGC exonic sequence...tcttttatgtgatttgcgttttggttaatctgtctctggtctttcaaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAAACACAGTTCAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46630.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
tcttttatgtgatttgcgttttggttaatctgtctctggtctttcaaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAA--ACACAGTTCAGG
| ||| || | || | | || || | | | || || || || | | | | | ||||| ||||||||||||||||||||||| || ||||||||||| ||||| || | || ||||| || ||||| || || | || || | | ||| |
-------------gtacgtgcagggaatgctaatatagaacctttttaacaca--taccagacag----ttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAGAAAAAAGTCCC--
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 12
tcttttatgtgatttgcgttttggttaatctgtctctggtctt--tcaaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAAACACAGTTCAGG-
|| || | ||||| | ||| | | || || | | || | | | || || ||||||||||||||||| ||||| ||||| || ||||||||||| ||||| || | || ||||| || ||||| || || | | || ||| || ||
-------------------------gtatgtgcaccaagtcttggtttgaaactttgtagcat-ctgagatggaaaatctcatagt--gatacattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTT-AGCAACAAATCCATACAAGAT
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 11
--tcttttatgtgatttgcgttttggttaatctgtctctggtct-ttcaaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAAACACAGTTCAGG
| | | || | | || | || | | ||| | | || | || | | || || ||| ||| || | ||| || ||||| ||||||||||| || ||||| || || ||||||||||| ||||| || ||||| ||||| |||||||| || |||| ||| | | ||
gtacgtatccgtcgca-acctactgttccattttcccctgttttctttcataactaagtg--attctattttcttta--tttactctctt----------cagGTGTGGGAGAAGAGTGGGTACAATACCGTTGAGTGGGTTCGTTACATTACAAAAGCAGGATCCTACGAGATTAGGTGCTAGACACAATTGGTATTTTGCT
upper sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA05G23670.1 (Glycine max), 3'ss of exon 12
-tcttttatgtgatttgcgttttggttaatctgtctctggtctttcaaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAAACACAGTTCAGG
| | | | | | || | | | || ||| ||| || | | | | || | ||| | | ||| || ||||| ||||||||||| || ||||| || || ||||||||||| ||||| || ||||| ||||| |||||||| || |||| ||| | | | ||
gtatccatcgcaacctaccgttcccct--ttttcctgcattctctcataactaggtgattctattttctttat-----ttactctctt----------cagGTGTGGGAGAAGAGTGGGTACAATACCGTTGAGTGGGTTCGTTACATTACAAAAGCTGGATCCTACGAGATTAGGTGCTAGACAGAGTTTGTATTACTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAAACACAGTTCAGG
acctgac putative branch site (score: 3)
tatactactttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttttatgtgatttgcgttttggttaatctgtctctggtctttcaaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAAACACAGTTCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - -gttttgg
- - - - - - - - - - - - - - - -gtctctg
- - - - - - - - - - - - - - - - - - - - - - caaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatccg