Sequence
atgc intronic sequence ATGC exonic sequence...gttcctgcatatgatttacttgagtgtgcacatcttttatgtgttgattgtctgatgtatcattataatatcaaatttctctctactttggacatttcagCTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA
Basic information
species | Glycine max |
transcript | GLYMA18G01960.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------gttcctgcatatgatttacttgagtgtgc-acatcttttatgtgttgattgtctga----tgtatcattataatatcaaatttctctctactttggac--attt--cagCTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA
|| || || ||| | | | | | || ||||||| | | | | || | |||| | | | | | | |||||| || || |||| |||||||||||||||| || ||||||||||||| |||||||||||
gtatgcaattctatttcactgagttccctaatcaggaaaatgcaacactcatgtgtagcattgatgtttctctttgatgagcttcatgtgttcagcttttaagttgtgcttttctatagtttgacaatgat-tctactctgcacctattttgcagCTTATCGGAAGCTCGCTAGGAGTTATCATCCAGATGTGAACAA
upper sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0324g00040.t01 (Vitis vinifera), 3'ss of exon 4
gttcctgcatatgatttacttgagtgtgcacatcttttatgtgttgattgtctgatgtatcatta-taatatcaaatttctctct--actttggacatttcagCTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA
| | | | | ||| ||| || ||| || | | || | || | | |||||| | || |||| | ||| | | || ||||||||| ||||||||| ||||||||||||| |||||||||||
---cttatgtgttacaaactgaagttgaagaattgtttttgcatagcctgctttatatccttgcactaatataaccttactctgtgtactcttcatcttgtagCTTATCGAAAGCTTGCCAGGAGTTATCATCCAGATGTGAACAA
upper sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0324g00040.t01 (Vitis vinifera), 3'ss of exon 7
gttcctgcatatgatttacttgagtgtgcacatcttttatgtgttgattgtctgatgtatcatta-taatatcaaatttctctct--actttggacatttcagCTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA
||| || | | || | || | | |||||| | || |||| | ||| | | || ||||||||| ||||||||| ||||||||||||| |||||||||||
----------------------------------gtttttgcatagcctgctttatatccttgcactaatataaccttactctgtgtactcttcatcttgtagCTTATCGAAAGCTTGCCAGGAGTTATCATCCAGATGTGAACAAMapped 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|21994326|gb|BQ785854.1|BQ785854EST: TTCTGTACTCGGGGTGTCAAGAAATTCCAGTAAATCTGAAATTAAGAATG CTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA
genomic: TTCTGTACTCGGGGTGTCAAGAAATTCCAGTAAATCTGAAATTAAGAATGgtaattgata ... gacatttcagCTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgtctgatgtatcattataatatcaaatttctctctactttggacatttcagCTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA
gtctgat putative branch site (score: 4)
atgtatcattataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcctgcatatgatttacttgagtgtgcacatcttttatgtgttgattgtctgatgtatcattataatatcaaatttctctctactttggacatttcagCTTATCGGAAGCTTGCCCGGAGTTATCATCCTGATGTGAACAA
- tcctgca
- - - - - - - - - - -gagtgtg
- - - - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - tctgatg