Sequence
atgc intronic sequence ATGC exonic sequence...ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaattatcaatttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
Basic information
species | Glycine max |
transcript | GLYMA07G00490.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaatta-tcaatttgttgtttattagctg-agtgttcttctttttgtcacct------cagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
||| | | || | | |||||| || ||| |||| || | | | || | | || || |||| ||||| || ||| |||||||||||||||||| |||||||| |||||||||| |||| |||||||| || || || ||||||||||||||||| ||||||||||||||||
------tttatttcttgtctgctacgtcttctataatta--tagcaaaaatggctctgctacatatataaccgttccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 1
ggaaaattt-----tgaagtgctatgtt-tcaaattctattgtttatcagccgaaattatcaatttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
|| || || || | ||| || | | | || | | | | | | | | ||||| | || | |||| | ||| ||| |||||||||| ||||||||||| ||||| ||||||| ||||| | || ||||| || || ||| |||||||| |||||| ||||| ||||||||||
ataatgcttgtcagctaactgttttgtgatcgtagttgaatgagttttattggcattcaatattttgtcaaggttctactaaaggttccttattta------ccagATTATGGCTGTGAAGAAGAATATAGAAGAGATACAAGGGAAAGACAGCTATCCATGGGGCCAACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATG
upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaattatcaatttgt---tgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
| |||| | | ||| || | | | ||| | || | || |||| ||| | || |||| || | || | ||||| || |||||||||||||||||| |||| | ||||| || || || ||||| |||||||| |||||||||||||| ||||||||||||||||
--agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctg-gaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 1
ggaaaattttgaagtgctatgtttcaaattctatt--gtttatc--agccgaaattatcaatttgttgtttattagctgagtgt-tcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
| | | || | | | | ||| | || |||| || || | | | | | | |||| | | | | | | |||| | || | ||||| || ||||||||||| |||||| |||||||||||| ||||| |||||||| ||||||||| ||||||||||||| || |||||||||||||
----actgctaaaattatgactcgcgaatccaatctggtttggtcaagttgattatgttagtcttcaaatcattaaatctgggcatgatgtgcttgtt-tttaagATAATGGCGGTGAAGAAGAATATAGAAGATTCACAAGGAAAAGACAATTATCCATGTGGGCAGCAATTGTTGATTCACAATGGAAAAGTTTTGAAAGATG
upper sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 1
ggaaaattttgaagtgctatgtttc----aaattctattgttta--tcagccgaaattatca-atttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
| | || || |||| | |||| ||| | | | | || | || || || | | | || || | | ||| | |||||||||| || ||||| || ||||||||||||||||||||||| || || || ||||| || ||||| ||||||| ||||| ||||| ||||||||||
-----actctgttcatctgtgttcccatgaaatatatttgcctgagtgtgttgcaaacaccacatgacttaatgaaaaccttggtaattgcttgttta--attgaagGTTATGGCGGTAAAGAAAAACATTGAAGATGTACAAGGAAAAGACAACTATCCGTGTGGGCAACAATTATTGATTCATAATGGAAAGGTCTTGAAAGATGMapped 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|298167381|gb|HO012644.1|HO012644EST: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
EST:
gi|13125598|gb|BG316168.1|BG316168EST: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACT GTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
genomic: AGACTTTGAAAGGGAGCCATTTCGAAATCAGGGTTCAACCCTCCGACACTgtcagtaatc ... gtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaaattatcaatttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
tgttcttctttttgtc CT-rich tract
ttatcaatttgttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaattatcaatttgttgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - tgctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtt