Sequence
atgc intronic sequence ATGC exonic sequencegtaagttctgaaaaatgtgctttgcttttaaaaacttgttaaggtttcgctctttgattgtctttcccacatcttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11670.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 6
-------------------------------gtaagttctgaaaaatgtgctttgcttttaaaaacttgttaaggtttcgctctttgattgtctttcccacatcttgatga-agGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
| |||| | || | | | | | || | || | | | || ||||| | | | |||||||| || ||||| ||||| |||||||| ||||| || ||||||||||| || ||||| || || ||||||||||| || | || || || || ||
gtatgtatcactcaagaaaaacagtgtgctctcaggttccatatcattt-catcatctgtgtttaccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 7
-----------------------------gtaagttctgaaaaatgtgctt---tgctttta-------aaaacttgttaaggtttcgctc-tttgattgtct-ttcccacatcttgatga-agGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
|||| ||| || || | ||| | || | | | || | | ||||||||||| | |||| | | | |||||||| || ||||||||||| ||||||||||| || || ||||| || ||||| || || ||||| ||||| ||||| |||||||| || || |||||
gtacaaaccagaactactcagctcagttgccgttttcttaaacatctgtctgcctgcctatatggcacggtgttatatcattgtcttgtcgatttgattgtctgtccccatgttccgtttccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGACCGCGGAGGCGCTAGCGATGGGCAAGTTCGTGGTGTGCGCCGACCACCCG
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 4
-------------------------gtaagttctgaaaaatgtgctttgcttttaaaaacttgttaaggtttcgctctttgattgtc-tttcccacat---cttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
| | || | ||| || | || | |||| || ||| || || | ||| | | || | |||||||| || |||||||| || ||||| || ||||| || ||||||||||| ||||| || || || |||||||| || ||| | || ||||| || ||
gtacgtatcaaacaagaaactttaaggcaattgtcaaagataattaattctgtattccacttttttttgttgattactgatgctgccatttgctgtttgtatttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAACGGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: AC233887.1_FGT006 (Zea mays), 3'ss of exon 6
--------------------gtaagttctgaaa-aatgt-gctttgcttttaaa---aacttgttaaggtttcgctctttgattgtctttcccacatcttga---tgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
| | || ||| | | |||| | || | | | | | || | | | | || | | |||| | |||||||| || || | || || || | || ||||| |||||||||||||| || || || || || |||||||| ||||| || ||||||||||| ||
gtgaggttctacgaagcatcaaagctactaaaacgacatcacttttatcttgatcttgtcctatgcaaattgctgattcaggtatctgttttcttctgttgaattttcagGTACAAGGTTTTTGTCAATCCAAGTGTTAGTGATGTGCTATGCACAGCAACAGCTGAGGCCCTTGCAATGGGGAAATTTGTAGTCTGTGCAGATCATCCA
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 6
-----gtaagttctgaaaaatgtgctttgcttttaaa---aacttgttaaggtttcgctc---------tttgattgtctttcccacat-cttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
| | ||| | | || || | | | || | || | | ||||||| ||| | | || || ||||||||||| || ||||| |||||||| |||||||| ||||||||||| || || || ||||| |||||||| || ||||| || ||||| ||||| ||
taaatgcacattcacctacacatgattctttctcatgctttacatacccagactccatctggaacttgttttgattaaatttggttcttatttattgtagGTACAAAGTCTTTATAAATCCCAGCATTAGCGATGTGCTATGCACAGCTACAGCTGAGGCACTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
upper sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
---------------gtaagttctgaaaaatgtgctttgcttttaaa---aacttgttaaggtttcgctctttgattgtctttcccacatcttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
| | | | | | | | || || | | |||| | |||| ||| | | ||| || ||||||||||| || ||||| || ||||| || ||||| ||||||||||| || || || || || |||||||| || ||||| || ||||| ||||| ||
acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaaacttgttaaggtttcgctctttgattgtctttcccacatcttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
tcttgat putative branch site (score: 4)
tctttcccacatctt CT-rich tract
ttgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttctgaaaaatgtgctttgcttttaaaaacttgttaaggtttcgctctttgattgtctttcccacatcttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA