Sequence
atgc intronic sequence ATGC exonic sequencegtctgtctttcctatttcatatgtttaatcctaggaatttgatcaattgattgtatgtatgtcgatcccaagactttcttgttcacttatatcttaactctctctttgctgtttctgcagAACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTGCCTGATCCAGATGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36010.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36010.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 9
gtctgtctttcctatttcatatgtttaatcctaggaatttgatcaattgattgtatgtatgtcgatcccaagactttcttgttcacttatatcttaactctctctttgctgtttctgcagAACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTGCCTGATCCAGATGAA
|| ||| || || |||| |||| | | |||| | | ||| | | || | | || ||| ||| || ||| |||||| ||||| ||||| || ||||||| |||||||| ||||||||||| || || ||||| ||||||
-------------gttgtctattttgaactctagtaatt--gttagatgatcctgt---tgttttttttatgagcaagtaaattaccaatacttta---------ctgtaattt--gcagAATCAGACACTGATCGCAATCAAAGCGCCTCATGGTACAACTTTGGAGGTCCCAGATCCTGATGAA
upper sequence: AT2G36010.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S97_96V6.1 (Physcomitrella patens), 3'ss of exon 9
gtctgtctttcctatttcatatgtttaatcctaggaatttgatcaattgattgtatgtatgtcgatcccaagactttcttgttcacttatatcttaactctctctttgctgtttctgcagAACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTGCCTGATCCAGATGAA
| ||| |||| |||| | | || | | || | | |||| | | ||| || | | | | || |||||| | || || || || | || ||||||| ||| || |||||||||||||| |||||||||||
-----------------ttttcgttagctcctcggaactagtctttttctgctgctttctgcaagttct---gctttagttcaaagttactgaatatgttcgtaatctgggcgtcggcagAATGAAACGCTTATTGCTATTAAGGCTCCTCTTGGGACCACTTTGGAAGTGCCAGATCCAGATGAG
upper sequence: AT2G36010.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S22_60V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------gtctgtctttcctatttcatatgtttaatcct---aggaatt-tgatcaattgattgtatgtatgtcgatcccaagactttcttgttcacttatatcttaactctctctttgctgtttctgcagAACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTGCCTGATCCAGATGAA
| | | | | || | | ||||| |||| || || | || | | ||||| | || | || ||| |||| | | | || | ||||||| | || || || || |||| ||||||| ||| |||||||| |||||||| |||||||||||
gtgagcacagagattctaccttggtgccattctggtgttgaatacatgatttggtgcaactttgcgatccttctaggacttatgtgctatccccctttttctgaaagatccgatattattgaagggtgctaatagcttaggtgttct----cggtgtttgcagAATGAAACGCTTATTGCTATCAAGGCTCCTCTTGGGACAACTTTAGAAGTGCCAGATCCAGATGAG
upper sequence: AT2G36010.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S364_42V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------gtctgtctttcctatttcatatgttta--atcctaggaatttgatca--attgattgtatgtatgtcgat-cccaagactttcttgttcactta---tatcttaactctctctttgct---gtttctgcagAACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTGCCTGATCCAGATGAA
| || || | || | || ||| | ||| | ||| | | | | | ||||| ||||| | | | ||| ||||| | || || | | |||| |||| |||||| |||| || || || |||| || |||| ||| ||||||||||||||||| |||||||||||
gtgagcacatctgtttttaatgcatcttacttataaaatcattttttgtaaactaatcttggcctagctccctacttcgctttggttatgaacctcgtaatatttctagaactcgtcttatgt-tgtcgttatttacaatcttcatgttctttcgaagtagctgagaaatacagatgcttgggttttggcagAATGAGACGCTTATTGCTATCAAGGCACCTCTTGGGACAACTTTGGAAGTGCCAGATCCAGATGAGMapped 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|164080923|gb|ES015386.1|ES015386EST: ATCAAGAGTTTACCAGGTTTCCAG AACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTG
genomic: ATCAAGAGTTTACCAGGTTTCCAGgtctgtcttt ... gtttctgcagAACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcccaagactttcttgttcacttatatcttaactctctctttgctgtttctgcagAACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTGCCTGATCCAGATGAA
tcttaac putative branch site (score: 2)
ctctctctttgctgtt CT-rich tract
ttatatcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtctttcctatttcatatgtttaatcctaggaatttgatcaattgattgtatgtatgtcgatcccaagactttcttgttcacttatatcttaactctctctttgctgtttctgcagAACCAGACTCTGATAGCCGTCAAAGCTCCTCATGGCACAACTTTGGAAGTGCCTGATCCAGATGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG