Sequence
atgc intronic sequence ATGC exonic sequencegtattattcattccattcttttttttttttttctcaagtttttcaattggttgttgttgttgtttaaagttttgatttttcgtggattttgattactgggtatgtttcaatttcgcagATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG
Basic information
species | Glycine max |
transcript | GLYMA09G28980.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 1
gtattattcattccattcttttttttttttttctcaagtttttcaattggttgttgttgttgtttaaagttttgatttttcgtggattttgattactgggtatgtttcaatttcgcagATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG
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-----------------gtgtgcgcctccttccactgatttatcgatttgcctaccctgtt-ttccccgttgggcgttctcatcgaattcccgagtttggctccgtgca--tgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 3'ss of exon 1
gtattattcattccattcttttttttttttttctcaagtttttcaattggttgttgttgttgtttaaagttttgatttttcgtggattttgattactgggtatgtttcaatttcgcagATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG
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--gtgagacatttgattgaatatggttcattggttaa---tttcattctagggttctcgagaattccttttttgagctct-gtttctttttctttctttcggggctcttttgttgcagATAAGAAATCA------GGGAAAGGTAAGATTGATGATGAAGACGTCACCTTTCAACGAATGGTTGCAAAG
upper sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 1
gtattattcattccattcttttttttttttttctcaagtttttcaattggttgttgttgttgtttaaagttttgatttttcgtggattttgattactgggtatgtttcaatttcgcagATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG
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----------------------gtattttcttttca-----ttgaat--gttagatttcatgtatgcatatacaactatgggagaaaatttcttatctgatttgaattgttgttgcagATAAGAAATGGGGAAAAGGGAAGGACAAAATTGATGATGAAGATATCACTTTCCAGCGCATGGTTGCCAAGMapped 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|18040197|gb|BM308491.1|BM308491EST: CATGGCAGGAAGAGAAGTTCGTGAATACACCAACCTCAGCGACCCCAAAG ATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTT
genomic: CATGGCAGGAAGAGAAGTTCGTGAATACACCAACCTCAGCGACCCCAAAGgtattattca ... aatttcgcagATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaagttttgatttttcgtggattttgattactgggtatgtttcaatttcgcagATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG
ttttgat putative branch site (score: 4)
ttttgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattattcattccattcttttttttttttttctcaagtttttcaattggttgttgttgttgtttaaagttttgatttttcgtggattttgattactgggtatgtttcaatttcgcagATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG