Sequence
atgc intronic sequence ATGC exonic sequence...atactcgttgtcaaaaaaatctttcttattttcctacgttgcccttctgattacaactttgccacacctctgcttctaattaatgtaaatgatactctagCAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACT
Basic information
species | Glycine max |
transcript | GLYMA09G05820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G05820.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
---------atactcgttgtcaaaaaaatctttctt-attttcctacgttgcccttctgattacaactttgccacacctc-tgcttctaattaatgtaaatgatactctagCAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACT---
| || ||| | | | | || | | | | |||| | || | || || || | | || | || | | |||||||||||| ||||||||||||||||||||||| || ||||| | |||| || || || ||||| ||||| |||||||||||||||||||||||||
gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA
upper sequence: GLYMA09G05820.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G06430.1 (Arabidopsis thaliana), 3'ss of exon 4
atactcgttgtcaaaaaaatctttcttattttcctacgttgcccttctgattacaactttgccacacctctgcttctaattaat-gtaaatgatactcta---gCAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACT---
|||| | || ||| | | | | | | || | | | | | || || | | || | ||| || || | || ||||||||| || |||||||| |||||||| || || || ||||| || |||| ||||| | ||||| ||||| || ||||| ||||||||||||||||
----------------gtatctcttctacactccca-gcttcagtatttttttctgttatcctaaactagtgaatgaacttgacagtatatcatcatttacttgcagATGGTGACAACATTTGGGATGTCTGAAATCGGACCATGGTCGCTAATGGATTCATCGGAGCAAAGCGATGTCATTATGAGGATGATGGCAAGAAACTCAA
upper sequence: GLYMA09G05820.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 3'ss of exon 4
atactcgttgtcaaaaaaatctttcttattttcctacgttgcccttctgattacaactttgccacacct--ctgcttctaattaatgtaaatgatactctagCAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTG---ATGTTATCATGAGAATGATGGCAAGAAACT
|| | | | || | || |||| || | || || || | || | || | | ||| | | | | ||| || | | ||||||||| ||||||||||| |||||||| || || || ||||| || ||||| | || ||||| |||| |||| |||||||||||||||||||| || |
---cttgctcttttaactaa-ttgcttaacaaataacaatttccctc-acctattatttggacaaatttaactgaatttgacgggtttaataaattcgtttgcagATGGTGACCACATTTGGGATGTCTGACATCGGCCCATGGTCGCTTATGGACACCTCGGCTCAGAGTGCTGATGTCATCATGAGAATGATGGCAAGGAATTMapped 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|11687680|gb|BF595356.1|BF595356EST: CAACTGGAGCAGTCGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG CAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTG
genomic: CAACTGGAGCAGTCGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... gatactctagCAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgattacaactttgccacacctctgcttctaattaatgtaaatgatactctagCAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACT
ttctaattaatgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atactcgttgtcaaaaaaatctttcttattttcctacgttgcccttctgattacaactttgccacacctctgcttctaattaatgtaaatgatactctagCAGATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - -cccttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttgcc