Sequence
atgc intronic sequence ATGC exonic sequence...ttcggatcatgaattactttttcttaaaccttcttccatttgattttaattgaacatacttgtgtttctaatcattattatcatcatttaaaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT
Basic information
species | Glycine max |
transcript | GLYMA11G37340.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G37340.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G175321_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------ttcggatcatgaattactttttcttaaaccttcttccatttgatt--ttaattga---acatacttgtgtttctaatcattattatcatcatttaaaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT
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gtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacga-actaacacaccgcatgcgtg-cagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC
upper sequence: GLYMA11G37340.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_71V6.1 (Physcomitrella patens), 3'ss of exon 3
ttcggatcatgaattactttttcttaaaccttc--ttccatttgattttaattgaaca--tacttgtgtttctaatcattattatcatcatttaaaaataat------agGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT
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---gtatcaaccactacaccacagccagttcacgtttccttcctattttccttccgccattgttcccttctccacaaactttgaggatgacgtgggtatcatgtttgtagGGGTCCAGGTCTCCTAATGCTCATCCTTTCATGGGTCATCACCCTCTTCACACTCTGGCAAATGGTGGAGATGCACGAAGCTGTGCCCGGAAAGCGATTC
upper sequence: GLYMA11G37340.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 2
-ttcggatcatgaattactttt--tcttaaaccttcttccatttgattttaattgaacatacttgtgtttctaatcattattatcatcatttaaaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT
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accctagtcgtgtgtcgcccgcaatcctccagctccatgttcttga---caaatggttttccaacttttccaagcaactttaaagatttttttttcgttccagGGGACCGGGGGTCCTTGTTCTTGTACTGTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT
upper sequence: GLYMA11G37340.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ25874 (Selaginella moellendorffii), 3'ss of exon 2
ttcggatcatgaattactttttcttaaaccttctt--ccatttgattttaattgaacatactt--gtgtttctaatcattattatc-atcatttaaaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT
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---gtgtcacccgcaa--tcctcaagaactttcacagccccatgttcttgacaaatcgttttccaacttttccaagcaactttaaagatttgtttttcgttccagGGGACCAGGGGTCCTGGTTCTTGTACTCTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT
upper sequence: GLYMA11G37340.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ10949 (Selaginella moellendorffii), 3'ss of exon 1
ttcggatcatgaattactttttcttaaaccttcttccatttgattttaattgaacatacttgtgtttctaatcattattat-catcatttaaaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT
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------------------------------------------gtaacgttcgaatgttataacgtctacattttttagggttcttcgttt-----ttccagGGGGCCTGGGATCTTCGTGCTCCTCCTCTCCTGGACCGTCACGCTCTACACGCTATGGCAAATGGTGGAGATGCACGAGATGGTGGAGGGCAAGCGCTTCMapped 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|192304931|gb|FG996091.1|FG996091EST: GTTGGTGCAGGTGTCCTCAGCCTTCCCTTTGCCATGTCAAATATGGGCTG GGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACAC
genomic: GTTGGTGCAGGTGTCCTCAGCCTTCCCTTTGCCATGTCAAATATGGGCTGgtacatgcat ... aaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaattgaacatacttgtgtttctaatcattattatcatcatttaaaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT
ttctaat putative branch site (score: 2)
tgtttctaatcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcggatcatgaattactttttcttaaaccttcttccatttgattttaattgaacatacttgtgtttctaatcattattatcatcatttaaaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - -catgaat
- - - - - - - - - - - - - - - ttcttcc