Sequence
atgc intronic sequence ATGC exonic sequencegtgattcatgccattttatactatttgcaactttgaggaccttatttagtatctgaagttgcacaactggaaaacgaagatgctatgtttaatggctttgttctgctttgtttttcagAAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTAACAGCATCCGTGTCTGATTTTCAGTGGAGCCAAAACTTTAAAGAACCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 4
---gtgattcatgccattttatactat--ttgcaactttgaggaccttatttagtatctgaagttgcacaactggaaaacgaagatgctatgtttaatgg-----ctttgttctgct---ttgtt-------tttcagAAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTAACAGCATCCGTGTCTGATTTTCAGTGGAGCCAAAACTTTAAAGAACCTC
| ||| | ||||| | || | || | || | ||| ||| || | | | || | | || | | | | ||| ||| | || || |||| | |||||||||||| |||||| | || ||||||| || ||||| ||||| || || |||||||| || |||||| ||||||||||||||||| | ||| | |
gttaggtttcttatcatttcaacctgtgattttcataacaagcatgccggcccgtacatga--ttttattattaaaagaaccatgtggttttctgagtggatcatgtttttcctactcacctgttggtgtcttctcagAAACAATTTTCAGAGCTACTTCTGAAAGCAGCAAGTGACTATGGGGCATTGACAGCATCTGTAGGTGATTTCCAGTGGAGCCAAAACTTCAGAGAGTCAC
upper sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 4
-------gtgattcatgccattttatactatttgcaactttgaggaccttatttagtatc--tgaagttgcacaactggaaaacgaagatgctatgtttaatggctt--tgttctgctttgtttttcagAAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTAACAGCATCCGTGTCTGATTTTCAGTGGAGCCAAAACTTTAAAGAACCTC
| || | | || | | | | | | | || | | | || || | | | | || | | | | ||| |||| ||| ||| | | || ||||||||||||||| ||| | || ||||||| || ||||| ||||| || || |||||||| || ||||| ||||||||||||||||||| ||| | |
gtaatttatttttgttcttgtcttgcaatttctatagcaattagcaaacaacatgataatgttggcctacccctaatgcattttcattgctttctttttgcctgcttaatgtgctgatct-cttgtcagAAACAATTCTCGGAGCTACTTCTGAAAGCAGCAAGTGACTATGGGGCATTGACAGCATCAGTCGGCGATTTCCAGTGGAGCCAAAACTTTAGGGAATCAC
upper sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G38820.1 (Glycine max), 3'ss of exon 4
gtgattcatgccattttatactatttgcaactttgaggaccttatttagtatctgaagttgcacaactggaaaacgaagatgctatgtttaatggctttgttctgctttgtttttcagAAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTAACAGCATCCGTGTCTGATTTTCAGTGGAGCCAAAACTTTAAAGAACCTC
| | | || || | | ||||| ||| | || || | | || || || | || || || | | |||| || || | |||||||||||||| || | || ||||| || || ||||||||||| || || |||||||| ||| | |||||||||||||| || || || || |||||||
---------------agaaaattgatgtaaatgttgaactattattgagtgt--aaattttaatcaatgcaagacaagcattgtaatgcctgtgtcatatttct-ctaatttgtgcagAAACAATTCTCTGAACTACTGATGAAGGCAGCTAGTGATTATGGTGCTTTGACAGCATCAGTGGCAGATTTTCAGTGGAGTCAGAATTTCAAGGAACCTCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125251747|gb|EL265832.1|EL265832EST: ATTGCATTCCAGTTGAAGCAGAATATCAG AAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTA
genomic: ATTGCATTCCAGTTGAAGCAGAATATCAGgtgattcatg ... tgtttttcagAAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTA
EST:
gi|116457559|gb|EG500151.1|EG500151EST: TCCAACAACCTTATTCGCTAGATTGCATTCCAGTTGAAGCAGAATATCAG AAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTA
genomic: TCCAACAACCTTATTCGCTAGATTGCATTCCAGTTGAAGCAGAATATCAGgtgattcatg ... tgtttttcagAAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactggaaaacgaagatgctatgtttaatggctttgttctgctttgtttttcagAAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTAACAGCATCCGTGTCTGATTTTCAGTGGAGCCAAAACTTTAAAGAACCTC
gtttaat putative branch site (score: 4)
ctttgttctgctttgt putative PPT
tatgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattcatgccattttatactatttgcaactttgaggaccttatttagtatctgaagttgcacaactggaaaacgaagatgctatgtttaatggctttgttctgctttgtttttcagAAACAATTCTCAGAGTTGCTAATGAAAGCCGCCAGTGATTATGGCGCCTTAACAGCATCCGTGTCTGATTTTCAGTGGAGCCAAAACTTTAAAGAACCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC