Sequence
atgc intronic sequence ATGC exonic sequencegtcagattttcccttgaagagaacttttcttactgatattcttaattcttttggaatgcatctaatgtagtgatgctctatctaagttagttctgttttgcctcatgatttagGCTGCAAATCCTGGTTGCATTTTGGAAGATTTTGTGAGATGGTACTCTCCTCCTGATTGGAGTGAAAGTGAGGGAAGTACTGAGGATAGAGATTCTTCTT
Basic information
species | Glycine max |
transcript | GLYMA08G43140.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G43140.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G55060.1 (Arabidopsis thaliana), 3'ss of exon 9
gtcagattttcccttgaagagaacttttcttactgat--attcttaattcttttggaatgcatctaatgtagtgatgctctatctaagttagttctgttttgc-ctcatgatttagGCTGCAAATCCTGGTTGCATTTTGGAAGATTTTGTGAGATGGTACTCTCCTCCTGATTGGAGTGAAAGTGAGGGAAGTACTGAGGATAGAGATTCTTCTT
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----gtgatcatcttaatgaataatcttattactgtttggtatataagcactc----atgtaaggaaagaaattgtagctgatatgaaattgataagatctgtacctctgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGTCTGGAGATGACTCTTCACCCG
upper sequence: GLYMA08G43140.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 9
gtcagattttcccttgaagagaacttttcttac------tgatattcttaat-----tcttttggaatg-catctaatgta----------gtgatgctctatctaagttagttctgttttgcctcatgatttagGCTGCAAATCCTGGTTGCATTTTGGAAGATTTTGTGAGATGGTACTCTCCTCCTGATTGGAGTGAAAGTGAGGGAAGTACTGAGGATAGAGATTCTTCTT
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gtgaagttttactgtgaagaaaatattattcatatttcttgatcctctagatgctgattttttgccttgatatatgaagaaaaaaacatgcgcaaggatcaatctgactgacttctattaattatcatgtcttagGCTGCAAATCCTGGATCTATTTTAGAAGATTTTGTGAGATGGCATTCACCGCCTGATTGGACTGATACTGAGCCTAGTGATGAGTTTAAAGACACCTTTG
upper sequence: GLYMA08G43140.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S73_65V6.1 (Physcomitrella patens), 3'ss of exon 11
---gtcagattttcccttgaagagaacttttctta--ctgatattcttaattcttttggaatgcatctaatgtagtga--tgctctatctaagttagttctgttttgcctcatgatttagGCTGCAAATCCTGGTTGCATTTTGGAAGATTTTGTGAGATGGTACTCTCCTCCTGATTGGAGTGAAAGTGAGGGA---AGTACTGAGGATAGAGATTCTTCTT
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gtaccttggttatctatcatggactatgattcgcaatttcatatcagctatcatgttttatgctttgcaattttgtaacttgtgtttttcaaaattatggttgtttggttttcgatttagGCTGCCAATCCCGGATGCATATTGGAGGACTTTGTGCGGTGGTACTCTCCTTTGGATTGGAGGGAGGAACCGGGATCTGGTCTCATGTTTCAAGGAAGTT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctaatgtagtgatgctctatctaagttagttctgttttgcctcatgatttagGCTGCAAATCCTGGTTGCATTTTGGAAGATTTTGTGAGATGGTACTCTCCTCCTGATTGGAGTGAAAGTGAGGGAAGTACTGAGGATAGAGATTCTTCTT
atctaat putative branch site (score: 3)
ttctgttttgcctc putative PPT
atgattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagattttcccttgaagagaacttttcttactgatattcttaattcttttggaatgcatctaatgtagtgatgctctatctaagttagttctgttttgcctcatgatttagGCTGCAAATCCTGGTTGCATTTTGGAAGATTTTGTGAGATGGTACTCTCCTCCTGATTGGAGTGAAAGTGAGGGAAGTACTGAGGATAGAGATTCTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT