Sequence
atgc intronic sequence ATGC exonic sequence...tgttctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54610.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
tgttctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG---
| ||| | | | || ||| | | | | | ||| | | || |||| | | | || | || | | || |||| |||||||||| | ||||| ||||||||||| |||||||| || |||||||| || || || || ||||||| | || | |
-ggtct-catttgattta-ctatggcccaaaatggagcccggcactctcttaatgtaaattttgcaatgtctctaatttgtcccatttatttatatcttacagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGTCTCTTTGGTTTCTACAAATCACA
upper sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
tgttctgcttctagcatatctacatacacacacacacacacacacacaaagactgatccttt---ttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG------
| ||| | | || | | | || || || | | | | || | | | | | | ||| ||| | || |||| ||| || || || || || |||||||| |||||||||||||| ||||| || || ||||| |||||||||| | | ||||| || |||| ||
------gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTG---CGGTTGGTGTCCCCTTGGATGCTTCAA
upper sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
tgttctgcttctagcata-tctacatacacacacacacacacacacacaaagactgatcctttt---tttacataatcatttctatcttttgact-cttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG-----
||||| | ||| | ||| | | | || || | |||| | || | | | | || | | ||| | ||| | |||||||| | ||||||| || |||||||| |||||||||||||| |||||||| |||||||| |||||||| || ||| | | | | || |
--------ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGT--TGGTTTTCCTTTAGGATCTTCAC
upper sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 6
----------------------------------------------tgttctgcttctagca-----------tatctacatacacacacacacacacac-----acacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG------
|| | | |||||| | || | || | | | | | |||| | | || || ||| || || | | || | | ||||||||| | |||||||| || |||||||| ||||||||||| || ||||| || |||||||| ||||||| ||| | || | || |||||
gtatgttaaagaaatttacttctattgttttatgcctttgaactgctgctttccttctaataaaattcattatcatttttattattgaaaatctgtatagttgtgattgaaagtataaaactaacgttgattaaaatttgctg-caatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATGAAGATGG-ACAGC--TTGGCTTTCCTTTGGGATCTTCTA
upper sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------tgttctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG------
| || | | | || | | | | | || | || | | || | |||| | | || | | ||||||||| | |||||||| || |||||||| ||||||||||| || ||||| || |||||||| ||||||| ||| | || | || |||||
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGG-ACAGC--TTGGCTTTCCTTTGGGATCTTCTA
upper sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 6
-------tgttctgct-tctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG------
| || | | | | ||||| ||| | || || || | || | | | || | | | || |||| ||| ||| | |||||||| | ||||||| || |||||||| ||||||||||| || ||||| || |||||||| |||||||| || | ||| | || |||||
actgatttattttacaatacaaagtatctgcatgataatgcatccagtcaaaactcaaaagtaaagatt-------aaatttgttactatgattt----cttctgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATCAAGATGGACAAG---TTGGTTTTCCTTTGGGATCTTCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG
ttttgac putative branch site (score: 3)
ctctt CT-rich tract
tttttttacataatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - ctgcttc
- - - - - - - - - - - -atacaca
- - - - - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - caaagac