Sequence
atgc intronic sequence ATGC exonic sequencegttagtttcaacaactttcttctctctctctcttttttttatggttccttggtttggattctgtttctgggttttgttgtgcttgctgtgttgtgtcataaagtcttgacctttttgcggattattcagGCGTTTGAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
Basic information
species | Glycine max |
transcript | GLYMA15G16060.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G16060.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G472231_T01 (Zea mays), 3'ss of exon 1
gttagt-ttcaacaactttcttctctctctctcttttttttatggttc-cttggttt----ggattctgtttctgggttttgttgtgcttgctgtgttgtgtcataaagtcttgacctttttgcggattatt-----------cagGCGTTTGAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
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gtaagaaccttatgcccttgctctcgctctgccttcttcctgcgctcgatttggtttccgtcgctccccttgttgaccggttcttcgttgggaatgggatttggccatttggggacttttctgtcgattccttctctgtcggtcagGCATTCGAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCA
upper sequence: GLYMA15G16060.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
gttagtttcaacaactttcttctctctctctcttttttttatggttccttggtttggattctgtttctgggttttgttgtgcttgctgtgttgtgtcataaagtcttgacctttttgcggatt--attcagGCGTTTGAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
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------gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataa-tttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCAMapped 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|208261468|gb|GE059123.1|GE059123EST: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCTGTCGCT GCGTTTGAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAG
genomic: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCTGTCGCTgttagtttca ... gattattcagGCGTTTGAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAG
EST:
gi|193410473|gb|FK380268.1|FK380268EST: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCTGTCGCT A
genomic: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCTGTCGCTgttagtttca ... gattattcag-
EST:
gi|193410473|gb|FK380268.1|FK380268EST: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCTGTCGCT A
genomic: CTGATATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCTGTCGCTgttagtttca ... gattattcag-
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgtgcttgctgtgttgtgtcataaagtcttgacctttttgcggattattcagGCGTTTGAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
tcttgac putative branch site (score: 3)
attattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttcaacaactttcttctctctctctcttttttttatggttccttggtttggattctgtttctgggttttgttgtgcttgctgtgttgtgtcataaagtcttgacctttttgcggattattcagGCGTTTGAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG