Sequence
atgc intronic sequence ATGC exonic sequence...taccttcatatatcctgtaggtttgccagtgttagtcttaatatagactctactttttcagagtaaaattttgattctttttccccccttgaaaatacagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCAATGGATATTAGTGGCGAGCAGCATCTTGACATA
Basic information
species | Glycine max |
transcript | GLYMA05G24610.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0178g00020.t01 (Vitis vinifera), 3'ss of exon 2
taccttcatatatcctgtaggtttgccagtgttagtcttaatatagac--tctactttttcagagtaaaattttgattctttttccccccttgaaaatacagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCAATGGATATTAGTGGCGAGCAGCATCTTGACATA
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tgtaaaatattaacttgtgaaattgc--gtttaatttttagtttgaatattccactaattcatggtttgttggtccgtgttcctttttgtttgaaagtgcagTTTGATGTGACTTTTCCTGCCGTTCCTTGTTCGGTACTCACTCTTGATGCCATGGATATTAGTGGAGAACAGCATCATGATATA
upper sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S54_13V6.1 (Physcomitrella patens), 3'ss of exon 2
taccttcatatatcctgtaggtttgccagtgttagtcttaatatagactctactttttcagagtaaaattttgattctttttccccccttgaaaat----acagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCAATGGATATTAGTGGCGAGCAGCATCTTGACATA
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---tttcgggccgtttgttcgagtggcatgtgtcctaagatcatagaagtcgatgatg-agtgcagaagctatttctaaattgtcgcttcgtaagtctttgcagTTGGACATTACGTTCTCGGCATTGGCGTGCTCTGTTGTCAGCTTAGATGCAATGGACATTAGTGGTGAGCAGCACCTGAATGTG
upper sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S72_188V6.2 (Physcomitrella patens), 3'ss of exon 3
taccttcatatatcctgtaggtttgcc-agtgttagtcttaatatagactctacttttt-cagagtaaaattttgattctttttccccccttgaaaatacagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCAATGGATATTAGTGGCGAGCAGCATCTTGACATA
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--cctgaattcaagatagatatgctccgagtgtgcatgggctttaagactaaacgaacagcagagtcttatgtatcaagttgtgtgatttatgtttttacagTTGGACATCACGTTCCCAGCATTGGCGTGTTCTATGGTCAGCTTAGATGCAATGGATATAAGTGGTGAGCAGCACCTCAATGTGMapped 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|208145013|gb|GD941266.1|GD941266EST: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAAT TTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGTTTAGATGCA
genomic: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAATgtaattattg ... gaaaatacagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCA
EST:
gi|213617044|gb|DB961524.1|DB961524EST: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAAT TTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCA
genomic: AGAGTAAGCTTTTGGTGGATACTTCAAGGGGAGATACCTTGCACATCAATgtaattattg ... gaaaatacagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactctactttttcagagtaaaattttgattctttttccccccttgaaaatacagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCAATGGATATTAGTGGCGAGCAGCATCTTGACATA
ttttgat putative branch site (score: 4)
ttttgattctttttcc CT-rich tract
agtaaaattttgattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taccttcatatatcctgtaggtttgccagtgttagtcttaatatagactctactttttcagagtaaaattttgattctttttccccccttgaaaatacagTTTGATGTCACTTTTCCTGCTGTTCGATGTTCAATACTCAGCTTAGATGCAATGGATATTAGTGGCGAGCAGCATCTTGACATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
-accttca
- - - - - - tcctgta
- - - - - - - - - - - - -ccagtgt