Sequence
atgc intronic sequence ATGC exonic sequencegtttgtattttactaatataattgttcattttttgtatttctgtttgatttttttttatgtattttcttaaatttgtatattttatttgaatagtatatgctgaatctatcaagttttaattcttgtttggttcatgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTTATTGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTATATGAATTTA
Basic information
species | Glycine max |
transcript | GLYMA08G40770.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 2
gtttgtattttactaatataattgttcattttttgtatttctgtttgatttttttttatgtattttcttaaatttgtatattttatttgaatagtatatgctgaatctatcaagttttaattcttgtttggttcatgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTTATTGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTATATGAATTTA
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----------------------------------gtatgt---tttgaattgcttcagcatac------agaccacaaaatattattcaactgtcttctaatgcatc-atcaa--ttaaactagcgtt-atttcatttt-cagGCAGAAGTTGATTTTCTTGGAAACCTTCAACATCCACACCTAGTGAAATTGGTTGGTTACTGCATCGAAGATGACCAAAGGTTGCTAGTGTATGAATTTA
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 2
gtttgtattttactaatataattgttcattttttgtatttctgtttgatttttttttatgtattttcttaaatttgtatattttatttgaatagtatatgctgaatctatcaagttttaattcttgtttggttcatgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTTATTGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTATATGAATTTA
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------------------------------------gtatgtttttattttttgttggtatactttgttgaaga-gtattattcagctctctgcta-atgcgtcactaagcaaagt---atcattgcttgttt------gcagGCAGAAGTTGATTTTCTTGGAAACCTTCAGCATCCACATCTAGTGAAATTGGTTGGCTACTGCATTGAAGATGACCAGAGGTTGCTTGTGTATGAATTTA
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------gtttgtattttactaatataattgttcattt-----tttgtatttctgtttgatttttttttatgtattttcttaaatttgtatattttatttgaatagtatatgctgaatctatcaagttttaattcttgtttggt-tcatgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTTATTGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTATATGAATTTA
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gtttgaaactttcctaatctattttatttcctatatggaattgaactcctttatttgttcttcccccactttgtgtttttcttcttttgtcttttgttttttgtttttgatttttgatttatctttttttag-aaatcccttttatgtcttggctcttctcaagtttaatctcattttgcagGCTGAAGTGAATTTCCTTGGTGACCTCATTCATCCTAATCTGGTCAAACTGATTGGTTATTGCATTGAAGATGATCAAAGGTTGCTAGTTTATGAGTTTAMapped 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|21889037|gb|BQ742250.1|BQ742250EST: CTGTAAAAACCCTCAACCATGATGGGCTCCAGGGTCATAAAGAATGGCTG GCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTT
genomic: CTGTAAAAACCCTCAACCATGATGGGCTCCAGGGTCATAAAGAATGGCTGgtttgtattt ... catgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatagtatatgctgaatctatcaagttttaattcttgtttggttcatgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTTATTGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTATATGAATTTA
ttttaat putative branch site (score: 3)
tatcaagttttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtattttactaatataattgttcattttttgtatttctgtttgatttttttttatgtattttcttaaatttgtatattttatttgaatagtatatgctgaatctatcaagttttaattcttgtttggttcatgtgacagGCTGAGGTAAATTATCTTGGTGATCTAGTTCATCCACACCTTGTTAAACTTATTGGTTACTGCATTGAAGATGATCAAAGGTTGCTAGTATATGAATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG