Sequence
atgc intronic sequence ATGC exonic sequencegtgtttgccctttgatcctaagtgttattgctttgcgttcgtgtttcttattttatcctgtggctttttgatatgcagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
Basic information
species | Glycine max |
transcript | GLYMA02G42560.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 22
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
gtgtttgccctttgatcctaagtgttattgctttgcgtt-cgtgtttcttatttta-----tcctgtggctttttgatatg-cagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
||| | || |||| || | ||| | | || || | | | || | || | ||| || | | ||| ||||| || ||| | ||||| ||||||||||| ||| | || |||||||||||||| ||||| ||||| || ||||| |||||||||||||||| ||
gtgaat-ccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 22
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
gtgtttgccctttga---tcctaagtgttattgctttgcgttcgtgtttcttattttatcctgtggctttttgatatg----cagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
||| |||||| | || | | | | || | || | | | ||| | |||| || | | | || | ||| ||||| || ||| | ||||| ||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| |||||||||||||||| ||
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgc-tattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 22
gtgtt-tgccctttgatcctaagtgttatt--gctttgcgttcgtgtttcttattttatcctgtggctt---tttgatatgcagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
||| | || || | | | || | | || | || | ||| | || ||| || | | || || | || | | ||| ||||| || ||||| ||||| ||||||||||| |||||||| |||||||||||||| ||||| ||||| || ||||| ||||||||||| || || ||
gtgatgtgtccct--accatatgccctgttcgggttcactttctttttacttcaattg-cttatgctttgcatgtggttttcagAAATCGACTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCTCTGGGTAAAATCATTATAGACMapped 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|209718673|gb|BW662739.1|BW662739EST: CGTTCATTACTGCCAGTGGAGCCCCTTGTGGAGGAATGTGAGAAGAGG-- -AATCGACTTCGTATGCTCACACAGTTCTTGGAACACCTTGTAAGTGAGGG
genomic: CGTTCATTACTGCCAGTGGAGCCCCTTGTGGAGGAATGTGAGAAGAGGTGgtgtttgccc ... tgatatgcagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGG
EST:
gi|209720996|gb|BW682475.1|BW682475EST: CGTTCATTACTGCCAGTGGAGCCCCTTGTGGAGGAATGTGAGAAGAGG-- -AATCGACTTCGTATGCTCACACAGTTCTTGGAACACCTTGTAAGTGAGGG
genomic: CGTTCATTACTGCCAGTGGAGCCCCTTGTGGAGGAATGTGAGAAGAGGTGgtgtttgccc ... tgatatgcagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttattgctttgcgttcgtgtttcttattttatcctgtggctttttgatatgcagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
ttttgat putative branch site (score: 4)
cttttt CT-rich tract
tgtttcttattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttgccctttgatcctaagtgttattgctttgcgttcgtgtttcttattttatcctgtggctttttgatatgcagGAATCGGCTTCGTTTGCTCACACAGTTCTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATTATCATTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG