Sequence
atgc intronic sequence ATGC exonic sequence...tctagaatcttacagtgcagggataaggattttttgcagttttctccatttttaaaacctacacttaattccttatgatgttttgttttgttgcttgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGGAAGATTATGTCCACAGAATTGGTCGAACTGGTCGTGCAGGGGCTAAAGG
Basic information
species | Glycine max |
transcript | GLYMA17G09270.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G09270.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g68320.4 (Oryza sativa), 3'ss of exon 8
tctagaatcttacagtgcagggataaggattt--tttgcagttttctccatttttaaaacctacacttaattcctta--tgatgttttgttttgttgcttgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGGAAGATTATGTCCACAGAATTGGTCGAACTGGTCGTGCAGGGGCTAAAGG
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----gagatcgacaatgttgatatcccagtttggtctgctgtggtcttcagggcaaaagtattatcttgattacatactcatcattttcttgttatttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTGAAGATTATATTCACAGAATAGGTCGAACTGGCCGCGCTGGTGCTAGTGG
upper sequence: GLYMA17G09270.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G362850_T01 (Zea mays), 3'ss of exon 9
tctagaatcttacagtgcagggataaggattttttgcagttt--tctccatttttaaaacctacacttaattcctta-tgatgttttgttttgttgcttgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGGAAGATTATGTCCACAGAATTGGTCGAACTGGTCGTGCAGGGGCTAAAGG
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--tggggatcgacaatgttgatgttccagcgtggtccagcatggtattcaggacaacacatcaattttgattaagtactgataatatttgttgat-tttgcagATGTGAAGGACATAAAGTGTGTGATAAATTATGATTTTCCAACAACTCTTGAAGATTATATTCACAGGATAGGTCGAACTGGCCGTGCTGGTGCTAGCGG
upper sequence: GLYMA17G09270.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 9
----tctagaatcttacagtgcagggataaggattttttgcagttttctccatttttaaaacctacacttaattccttatgatgttttgttttgttgcttgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGGAAGATTATGTCCACAGAATTGGTCGAACTGGTCGTGCAGGGGCTAAAGG
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ttacacaaagaaatttctgttcttcttcctgcattt----catctcagtctatgatttacttctcaactgtgttccttctttcttcttttgttttgttttacagATGTGAAGGACATTAAATGTGTGGTTAATTATGATTTCCCAAATACATTGGAGGATTACATCCATAGGATTGGTCGAACCGGGCGTGCAGGAGCTAAAGGMapped 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|192314017|gb|FK011109.1|FK011109EST: TGGCAGAAGTCCAATAATGACTGCCACTGATGTTGCTGCACGGGGTCTTG ATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGG
genomic: TGGCAGAAGTCCAATAATGACTGCCACTGATGTTGCTGCACGGGGTCTTGgtaggatcac ... ttgcttgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatttttaaaacctacacttaattccttatgatgttttgttttgttgcttgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGGAAGATTATGTCCACAGAATTGGTCGAACTGGTCGTGCAGGGGCTAAAGG
acttaat putative branch site (score: 4)
ttttgtt putative PPT
ttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctagaatcttacagtgcagggataaggattttttgcagttttctccatttttaaaacctacacttaattccttatgatgttttgttttgttgcttgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGGAAGATTATGTCCACAGAATTGGTCGAACTGGTCGTGCAGGGGCTAAAGG
- - - - - tacagtg
- - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg