Sequence
atgc intronic sequence ATGC exonic sequence...acgtggcatttccttttaataaataaaaagataaaaaaaatgatgatatttatagaatatgtcaactgggtaattcttaattttaaatttgtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC
Basic information
species | Glycine max |
transcript | GLYMA07G05170.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 2
acgtggcat-ttccttttaataaataaaaagataaaaaaaatgatgatatt-tatagaatatgtcaactgggtaattcttaattttaaatttgtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC
| || | |||| || | || | || | | | || | | || | | | || | || | || ||| |||| ||||| || |||||||| ||||||||||| |||| ||| |||||||| ||||
--gctctatgctagttttcatggtttttggtctaggataagtttttttcttatgaatgttactttggaagtatctttgacatgttctgttctggattgctagGAACCAGTCTCGCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTTGAATGGC
upper sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G17280.1 (Arabidopsis thaliana), 3'ss of exon 2
---acgtg-gcatttccttttaataaataaaaagataaaaaaaatgatgatatttatagaatatgtcaactgggtaattcttaattttaaatttgtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC
| || | || | | || | | | | || | || | | | | | | | | || || || || || ||| | |||| ||||| || |||||||| ||||||||||| |||| ||| ||||| |||||||
tctatatgtgaatgttttcttggtt--ttggtttagagtaagtttcatattttcttttg--tttctttgggggttatttaatatgttctgtttttggcctttagGAACCAGTCTCCCATGTTGTTGCTCGTCCTTCCCCAAATGACATTCTCGAGTGGC
upper sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g00280.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------acgtggcatttccttttaataaataaaaagat---aaaaaaaatgatgat--atttatagaatatgtcaactgggtaattcttaattttaaatttgtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC
|| || | || || | ||| | ||| || | |||| ||| | | || || | || | || | ||| | || | |||||||| |||||||| ||||| || || || ||||| |||| |||||||||||||||||
gtatgccttcttaatatgcccttttaaattgtataaataactactaattatatagttatagcacatatgcattctggaaatgaacttttgatttgtttttcttttgggttaaatttgttaatcatgctttcta---tgaacttgcagGAACCAGTTTCCCATGTGGTTGCCCGCCCTTCCCCAAATGATATTCTTGAGTGGCMapped 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|298173240|gb|HO020224.1|HO020224EST: AGAAATCATGCATCAAGCGCCTTCAGAAGGAATATAGAGCCCTTTGTAAA GAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCGAGTGATATTCTTGAG
genomic: AGAAATCATGCATCAAGCGCCTTCAGAAGGAATATAGAGCCCTTTGTAAAgtatgtacag ... gtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAG
EST:
gi|298163944|gb|HO013589.1|HO013589EST: AGAAATCATGCATCAAGCGCCTTCAGAAGGAATATAGAGCCCTTTGTAAA GAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAG
genomic: AGAAATCATGCATCAAGCGCCTTCAGAAGGAATATAGAGCCCTTTGTAAAgtatgtacag ... gtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatttatagaatatgtcaactgggtaattcttaattttaaatttgtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC
tcttaat putative branch site (score: 3)
taattcttaattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acgtggcatttccttttaataaataaaaagataaaaaaaatgatgatatttatagaatatgtcaactgggtaattcttaattttaaatttgtatttgcagGAGCCAGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC
- - -gcatttc
- - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcaac