Sequence
atgc intronic sequence ATGC exonic sequencegtatgagttctttatcacctctatacctcttgactgtgataactgtttaaggaagttggtctgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTCGGGACTTCTTGGTGCATTTTCTTGGAGTTTGATGGCTGGTTTTGTTGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32040.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G28510.1 (Glycine max), 3'ss of exon 4
---------------------------------------------gtatgagttctttatcacctctatacctcttgactgtgataactgt-ttaaggaagttggtc---tgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTCGGGACTTCTTGGTGCATTTTCTTGGAGTTTGATGGCTGGTTTTGTTGAC
|| | ||| ||| | | | || || | | | ||| ||| || | || ||||||||||| || || || |||||||||||||| |||||||| |||||| | || || || ||||||||| | || ||||||||||||||| ||||||||||
gtgagtctaaaactgcatcactttttcctcttcctgaaatgagtggttcattatttttctcaattttgtcaatcctggggaccacattttcattattgaacttaataatatggcatgcagTGATTCTGTCCCCCTCTTTGGTTATCGAAGAAGGTCATACCTAGTTTTGTCAGGGCTGCTTGGTGCACTCTCGTGGAGTTTGATGGCTACTTTTGTTGAC
upper sequence: AT2G32040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G39220.1 (Glycine max), 3'ss of exon 3
------------------------------------------------gtatgagttctttatcacctctatacctcttgactgtgataac-tgtttaaggaagttggtctgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTCGGGACTTCTTGGTGCATTTTCTTGGAGTTTGATGGCTGGTTTTGTTGAC
|| | || | | || ||| | |||| | | | || | | || | || ||||||||||| || || || |||||||||||||| || || || |||||| | || || || |||||||| | || ||||||||||||||| ||||||||||
gtgagtctaaaactgcatcactttttcctctctcctgaaatgagtggttcattattttctcaattttattaatcctgtggactacattttcattattgaagttattaatatggcatgcagTGATTCTGTCCCGCTCTTTGGTTATCGAAGAAGATCGTACCTAGTTTTGTCAGGGCTGCTTGGTGCGCTCTCATGGAGTTTGATGGCTACTTTTGTTGAC
upper sequence: AT2G32040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g03660.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------gtatgagttctttatcacctctatacctcttgactgtgataactgt-ttaaggaagttggtctgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTCGGGACTTCTTGGTGCATTTTCTTGGAGTTTGATGGCTGGTTTTGTTGAC
| | || || | | || || | ||| || ||| || | |||| | | | |||||| ||||| | || || |||||||||||||| |||||||| | ||||| || || |||||||| ||| | || |||||||||||||| |||||| |||
gtgccggcctattcctttatctccattgttttcccttaattgataaatacatgtttcctatttgtt-tatttgtgtttaataagtgtttatttattgcagCGATTCTTTACCACTTTTTGGTTATCGAAGAAGGTCATACTTGGTTCTATCAGGGCTTCTTGGAGCACTCTCATGGAGTTTGATGGCCACTTTTGTGGACMapped 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|124731938|gb|EH823340.1|EH823340EST: GGTCTTTCTTCATTGCCGTGGCTTGTTAAGCCTCTCTATGGTTTTATCAG TGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTC
genomic: GGTCTTTCTTCATTGCCGTGGCTTGTTAAGCCTCTCTATGGTTTTATCAGgtatgagttc ... tgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTC
EST:
gi|116448948|gb|EG491540.1|EG491540EST: GGTCTTTCTTCATTGCCGTGGCTTGTTAAGCCTCTCTATGGTTTTATCAG TGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTC
genomic: GGTCTTTCTTCATTGCCGTGGCTTGTTAAGCCTCTCTATGGTTTTATCAGgtatgagttc ... tgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctctatacctcttgactgtgataactgtttaaggaagttggtctgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTCGGGACTTCTTGGTGCATTTTCTTGGAGTTTGATGGCTGGTTTTGTTGAC
tgataac putative branch site (score: 2)
tctgtttt putative PPT
tgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagttctttatcacctctatacctcttgactgtgataactgtttaaggaagttggtctgttttgcagTGATTCAGTGCCTCTATTTGGTTATCGAAGGAGGTCATATCTAGTTCTCTCGGGACTTCTTGGTGCATTTTCTTGGAGTTTGATGGCTGGTTTTGTTGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG