Sequence
atgc intronic sequence ATGC exonic sequence...gtgtaaggagggcaattgctcttggataacttttattaaaagaacctaaagttatggataatgagtatttctcacttggttgcactctctcttttcccagGTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGAAGAATC
Basic information
species | Glycine max |
transcript | GLYMA06G36130.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G36130.4 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G027756_T01 (Zea mays), 3'ss of exon 1
gtgtaaggagggcaattgctcttggataacttttattaaaagaacctaaagttatg-gataatgagtatttctcacttg--gttgcactctctcttttcccagGTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGAAGAATC
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--ttaaaatttcccatgagttgtacttca-tattatttctgttgcctcatgttttatgttgaatctcattgcttactcaaagtcctgtgttatctttttgtagGTTTGACAAGGAACTGAATAAAGAGGTTGCTATAAAAGTCATTGATTTGGAAGAAGC
upper sequence: GLYMA06G36130.4 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 2
----gtgtaaggagggc--aattgctcttggataacttttattaaaagaacctaaagttatggataatgagtatttctcacttggttgcactctctcttttcccagGTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGAAGAATC
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aaatatatcaagctggttaagttgtttattattgaatctgttttgggaagtctgcttgcacatgaggccagtggcccctaatac------ctcttcttgtttgcagGTTTGATAAAGAGCTTAACAAAGATGTTGCTATTAAAGTAATTGATTTGGAAGAAGC
upper sequence: GLYMA06G36130.4 (Glycine max), 3'ss of exon 1
lower sequence: EFJ15774 (Selaginella moellendorffii), 3'ss of exon 1
---gtgtaaggagggcaattgctc---ttggataacttttattaaaa---gaacctaaagttatggataatgagtattt-ctcacttggttgcactctctcttttcccagGTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGAAGAATC
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gttagttctcgctcctccttgctcgcgttgcagatcgattgctaggttttggatctaccattcttgtcttggagccctaattttcgtgaattggttttctttgctcgcagCTTTGACAAGGAGCTCAACAAGGAGGTTGCTATCAAAGTCATTGATCTCGAAGAAGC
upper sequence: GLYMA06G36130.4 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 1
---gtgtaaggagggcaattgctc---ttggataacttttattaaaa---gaacctaaagttatggataatgagtattt-ctcacttggttgcactctctcttttcccagGTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGAAGAATC
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gttagttctcgctcctccttgctcgcgttgcagatcgattgctaggttttggatctatcattcttgtcttggagccctaattttcgtgaattggttttctttgctcgcagCTTTGACAAGGAGCTCAACAAGGAGGTTGCTATCAAAGTCATTGATCTCGAAGAAGCMapped 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|213611344|gb|DB972745.1|DB972745EST: AGTTCACTGGAGCTCATTGGACAGGGATCATTTGGCGATGTGTACAAAGG GTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGA
genomic: AGTTCACTGGAGCTCATTGGACAGGGATCATTTGGCGATGTGTACAAAGGgtaagtgttt ... cttttcccagGTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaagttatggataatgagtatttctcacttggttgcactctctcttttcccagGTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGAAGAATC
ttctcac putative branch site (score: 2)
ttgcactctctctttt putative PPT
ataatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtaaggagggcaattgctcttggataacttttattaaaagaacctaaagttatggataatgagtatttctcacttggttgcactctctcttttcccagGTTTGACAGGGAGCTCAACAAAGAAGTTGCTATCAAAGTGATTGATTTGGAAGAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA