Sequence
atgc intronic sequence ATGC exonic sequencegtagccacatgaaataattagttttgttggaggtcatttcagcctgcaattctagaatattgttttttgcaaaatcatttctggttcaatatgagtttttggctgaaaattgatgcatttgacttgcagAGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATTGAACTGTGATGGTGCTGAGGATGTAATTATTGCTGTTAATTCAACCAAG
Basic information
species | Glycine max |
transcript | GLYMA11G20520.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 10
gtagccacatgaaataattagttttgttggaggtcatttcagcctgcaattctagaatattgttttttgcaaaatcatttctggttcaatatga-gtttttggctgaaaattgatgcatttgacttgcagAGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATTGAACTGTGATGGTGCTGAGGATGTAATTATTGCTGTTAATTCAACCAAG
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---------------------------------------------gtatgtccaggatataaacttctttcgcttc--tactgtttatattggatgttttttattctaacacattactatgcccatttagAGGCTTCAATGATGCTATAAGTGGTTTCAATGATGATGGTTGGTCTGTCATGGGTGGGGATGGCATTGAAGATGTGATCATTGCTTGCAATGCAAAGAAG
upper sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 10
gtagccacatgaaataattagttttgttggaggtcatttcagcctgcaattctagaatattgttttttgcaaaatcatttctggttcaatatgagtttttggctgaaaattgatgcatttgacttgcagAGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATTGAACTGTGATGGTGCTGAGGATGTAATTATTGCTGTTAATTCAACCAAG
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gtggctgtac--aatctttctttctttcc----ttttttctgattccagcatcacattat--tcatctgtaaa------tttgact-aatat----ttttgtc---atattttt-catttt-cctgcagAGGCTTCAATGATGCTATCAACGGATTTAATGATGACGGCTGGTCATTGATGAGTTGTGATGGTGCTGAAGATGTAATAATTGCAGTTAACTCAACCAAA
upper sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ37565 (Selaginella moellendorffii), 3'ss of exon 10
gtagccacatgaaataattagttttgttggaggtcatttcagcctgcaattctagaatattgttttttgcaaaatcatttctggttcaatatgagtttttggctgaaaattgatgcatttgacttgcagAGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATTGAACTGTGATGGTGCTGAGGATGTAATTATTGCTGTTAATTCAACCAAG
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-------------------------------------------------gtctgtcattttgtgtttcttttcattctttctttctttatgggacttctttgttt----ttcttg---ttga--gacagAGGCTTCAATGACGCTGTAAATGGATTTCCAGACGATGGATGGTGCACTATGGGTGGCGATGGCTTGGACAATGTAGCTGTCAGCTGCAATGCCACGATAMapped 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|27426486|gb|CA938006.1|CA938006EST: CTGCTGTTCTGCGGACTTTCAGCCAGAGATTGAGCAG AGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATT
genomic: CTGCTGTTCTGCGGACTTTCAGCCAGAGATTGAGCAGgtagccacat ... tgacttgcagAGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATT
EST:
gi|14516259|gb|BI094931.1|BI094931EST: TGGGTAGGCATGTCTGCTGTTCTGCGGACTTTCAGCCAGAGATTGAGCAG AGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATT
genomic: TGGGTAGGCA-GCCTGCTGTTCTGCGGACTTTCAGCCAGAGATTGAGCAGgtagccacat ... tgacttgcagAGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttctggttcaatatgagtttttggctgaaaattgatgcatttgacttgcagAGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATTGAACTGTGATGGTGCTGAGGATGTAATTATTGCTGTTAATTCAACCAAG
atttgac putative branch site (score: 4)
aaaattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagccacatgaaataattagttttgttggaggtcatttcagcctgcaattctagaatattgttttttgcaaaatcatttctggttcaatatgagtttttggctgaaaattgatgcatttgacttgcagAGGCTTCAATGACGCTGTAAATGGATTCAATGATGATGGGTGGACTGTATTGAACTGTGATGGTGCTGAGGATGTAATTATTGCTGTTAATTCAACCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT