Sequence
atgc intronic sequence ATGC exonic sequence...tatttaagggggtaatggggtgtcatatatgattaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactccttttctatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC
Basic information
species | Glycine max |
transcript | GLYMA13G03430.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 4
tatttaagggggtaatggggtgtcatatatgattaaag-atagacatactcataag--ctaaatgcaaattctcataaatgtgttactccttttctatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC
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----------------gtaacgcaatgaatgattcaggcatttacaatgtccggagtaccagttaatgatatgttttgatgtggt----ctgtgtgttctcagGTACCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTCAGAACACATGTGCTCACAGAGCCTGCCCTC
upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 4
tatttaagggggtaatggggtgtcatatatgattaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactccttttctat-ctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC
||| || | | ||| || || | | || | | | || | | ||| | | || || | || || ||||| | |||||||| ||||||||||| | ||||| || || ||||| || ||||||| ||||||||||| |||||| ||||| || ||||| |||||||
---gtaaaaacaacgtgcgat-tcaggcatttttttacgaggtcagagttagcagttgcag--aaacttatgtttatttgatgtggtttgcgcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGATGGGAGACCTGGATGTGTTATGAACACATGTGCTCACAGAGCTTGCCCTC
upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 4
tatttaagggggtaatggggtgtcatatatgattaaagatagacatactcataagctaaatgcaaattctcataaatg-tgttactccttttctatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC
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-------gtatgtatagtggt-tcttgcttgatttaag--cgtctt--ccattagttacaagc---ttctgagaaatgctattgtttatttctta----agGTACCAATTGAATGCTTTGAACAACCATGGGTTATCTTTAGGGGTGAAGACGGGAAACCAGGATGTGTACGGAATACATGTGCGCATAGAGCATGTCCTC
upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------------------------tatttaagggggtaat--ggggtgtcatatatgattaaagatagacatactcataagctaaatgcaaattctc---ataaatgtgttactccttttctatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC
| | | | | | ||| | | | | | ||| || | | | | || | || || ||| || || | |||||| | |||||| ||||| || || ||||||||||| |||||| ||||||| ||| |||||||||| ||||||||||| | |||||||| || |||||||| |||||||
gtaagccagttttccaaacatctaaggctcatatttagtgattaaatacagattttccacattgtggctactcaacaatgtcttaagtagcaataagagaggaggcaaacatttatagcttatctggccttgtgataatctgtgagttttccttgtaacagttttcacctttttctgtttcagATTCCAATTGATTGCTTTGAGGAACCGTGGGTTGTCTTTCGTGGGCAAGATGGGAAACCTGGATGTGTCCGTAACACCTGCGCCCATAGAGCATGCCCTC
upper sequence: GLYMA13G03430.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S290_42V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------tatttaagggggtaatggggtgtcatatatgattaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactcctttt--ctatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC
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gtgaagaccactcgtgactttttgtccagtattgtacatgcgttgtgaatctttgtctggtctttcaacagcctggccatgaacttatttgtcgctttaccctggcttaacgaaaggttgatcctgtaatgagctgtatcagGTGCCGTTTAATAGCTTTGAAGAAGCATGGGTTATTTTTCGAGGGAAAGATGGCCGTCCAGGATGCGTGCGAGATTCTTGCGCACACAGGGCATGTCCACMapped 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|17153877|gb|BM143810.1|BM143810EST: ATTTCTGGTATCCTGTTGCTTTTTCTAATGACCTAAAGGATGATACCATG ATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGAT
genomic: ATTTCTGGTATCCTGTTGCTTTTTCTAATGACCTAAAGGATGATACCATGgtaagtcaat ... tctatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactcataagctaaatgcaaattctcataaatgtgttactccttttctatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC
agctaaa putative branch site (score: 3)
ttactccttttctatc putative PPT
aaattctcataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttaagggggtaatggggtgtcatatatgattaaagatagacatactcataagctaaatgcaaattctcataaatgtgttactccttttctatctcagATCCCAATAGAATGTTTTGAGGAACCATGGGTTATCTTTCGAGGGAAAGATGGGAAGCCTGGATGTGTGCAGAACACCTGTGCACATAGAGCCTGCCCTC
- - - -gggggta
- - - - - - - -tggggtg
- - - - - - - - - - - - - - - - - - - - - -catactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcaa