Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgcttcatctcacttgtgggggaaaaagcaattaaaataacatttatggactaaaatggtggtgcaaatattgtgatccacatgatggcttattgtgcatgtctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTAGATGTGGACCACATAGATGATCGAAGACTCTGCTGTGGT
Basic information
species | Glycine max |
transcript | GLYMA12G31980.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g38050.1 (Oryza sativa), 3'ss of exon 9
gtgagtgcttcatctcacttgtgggggaaaaagcaattaaaataacatttatggactaaaatggtggtgcaaatattgtgatccacatgatggcttattgtgcatgtctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTAGATGTGGACCACATAGATGATCGAAGACTCTGCTGTGGT
|| || || | ||| | ||| || | ||| ||| ||| | | || | | | ||| || | || | ||| ||| ||||||| ||||||||||| ||||| ||||||||||| ||| |||| | ||||| || || ||||| || || ||| | |||||||| || || ||||| |||
gtaagaaatttct-tcagatttggtt----------tttctttgttgattacaccataatatgttttatctaacctc----tacccatcattgaccatggatgatggtgatgtttcagGCATGTTCTCCACAAATATGCTAATGAGGATGTATCATTAGGAGCATGGTTCATAGGTCTAGACGTCGAACACGTCGATGATCGCAGGCTTTGCTGCGGT
upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagtgcttcatctcacttgtgggggaaaaagcaattaaaataacatttatggactaaaatggtggtgcaaatat-tgtgatccacatgatggcttattgtgcatgtctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTAGATGTGGACCACATAGATGATCGAAGACTCTGCTGTGGT
||| |||| | | | || ||| | || | | | ||| | | || ||| |||||| ||||| ||||| ||||| ||||||||||| || ||||| |||||||||| || || |||||| || || |||||| ||||||| || |||||
-----------------------------------------gtaagatttgaactcctttgtaccgcatcatttatgcctcattctccatctaacttctcttacaaa---atgttccagGCATGTTCTGCACAAATATGCAAATGAGGATGTTACATTAGGTGCTTGGTTTATCGGGCTTGATGTGACACATATCGATGATAGAAGACTATGTTGTGGC
upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 9
gtgagtgctt-catctcacttgtgggggaaaaagcaattaaaataacatttatggactaaaatggtggtgcaaatattgtgatccacatgatg-gcttattgtgcatgtctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTAGATGTGGACCACATAGATGATCGAAGACTCTGCTGTGGT
|| ||| | | | || || ||| ||| | | | | ||| |||| | | | | | ||||| | ||||| | | | ||||| || | | || | |||||| ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||| || |||| ||| || || |||||||| ||| | || |||||
gtaagttttcacttaccattttcaaggggtaaaaaaggaatcagcaaattcttggattgatgtatt--tcataatatcctcttccactttttatggttattttgtacatgattattgcagGCATGTTCTTCACAAGTATGCTAATGAGGACGTTTCACTGGGTTCTTGGTTTATTGGTCTTGATGCGGAACATATTGATGATCGGAGATTATGTTGTGGCMapped 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|20498515|gb|BQ273445.1|BQ273445EST: CAGTTGTATGCCATTTCAAAAGATCTGGCTACATATATTTCAAATAACAA GCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTT
genomic: CAGTTGTATGCCATTTCAAAAGATCTGGCTACATATATTTCAAATAACAAgtgagtgctt ... tttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggtgcaaatattgtgatccacatgatggcttattgtgcatgtctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTAGATGTGGACCACATAGATGATCGAAGACTCTGCTGTGGT
tctttgtctc CT-rich tract
aaatattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgcttcatctcacttgtgggggaaaaagcaattaaaataacatttatggactaaaatggtggtgcaaatattgtgatccacatgatggcttattgtgcatgtctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTAGATGTGGACCACATAGATGATCGAAGACTCTGCTGTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA