Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatctgttaaatatttacaatcgttttatttttcaaaatcttaacatatatcatctatttcagCATCAAGATGGAAAGATTCACACTCTGGCCAGCATGTTGAATATGATCAAAGGCCAGATGTATTTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03940.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g57940.4 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------------------------------------------gtgagtatctgttaaatatttacaatcgt-tttatttttcaaaatcttaacatatatcatctatttcagCATCAAGATGGAAAGATTCACACTCTGGCCAGCATGTTGAATATGATCAAAGGCCAGATGTATTTAG
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gtaggcttttgttcaaagtagtctcatctgtgtatgaagtattcaatttagttctcaatgtgctatggcatttgctcttatgcattttgtacttgaatcccaaggaattgttgccctgttgatttatttttatttcgtgatgttgaaatcatg-cagCATCCAGGTGGAAAGAAGCATCATCTGGTCAGCATGTTGACTATGATCAGAGGCCAGATGTCTTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------------------------------------------------gtgagtatctgttaaatatttacaatcgttttatttttcaaaatcttaa-----cata-tatcatct---atttcagCATCAAGATGGAAAGATTCACACTCTGGCCAGCATGTTGAATATGATCAAAGGCCAGATGTATTTAG
|| ||||| || || ||| || || | | || || ||| || ||| | ||||||||||| | |||||| || | | ||| ||||||||||| ||||||||||||||||| |||||||
gtatgcaatggaaaccttatgtgattgatactggttgcaaaaattgagcacataacccatctcaataagatttaacattccctaatcagaattgcggatgttcttttgtaatgctgtttg-tacctaatatcattgtaaaatgtgagttcacaagtgctcatgctaccatttacaatttcagCATCTAAATGGAAGGAAACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S39_28V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------gtgagtatctgttaaatatttacaatcgt---tttatttttcaa-aatcttaacatatatcatctatttcagCATCAA---GATGGAAAGATTCACACTCTGGCCAGCATGTTGAATATGATCAAAGGCCAGATGTATTTAG
||||| | | ||| | || | | |||| || || ||| | | | || | || | ||| | | |||||| ||| | |||| |||||||| ||||||||||||||||| |||||||| |
gaagagcatctgcactgagaattggatgagtttattaccgctatgtccatgcacaagtcaatttcacaccaagattatcgtctttctttcatatatgcagCTACTCGATGGAGGGATGGTACCACTGGTCAGCATGTAGAATATGATCAAAGGCCTGATGTATTCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatatttacaatcgttttatttttcaaaatcttaacatatatcatctatttcagCATCAAGATGGAAAGATTCACACTCTGGCCAGCATGTTGAATATGATCAAAGGCCAGATGTATTTAG
tcttaac putative branch site (score: 2)
tctatttc putative PPT
ttttatttttcaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatctgttaaatatttacaatcgttttatttttcaaaatcttaacatatatcatctatttcagCATCAAGATGGAAAGATTCACACTCTGGCCAGCATGTTGAATATGATCAAAGGCCAGATGTATTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG