Sequence
atgc intronic sequence ATGC exonic sequencettggccttggtaaagttaggacatgtttgccttagtaagatgagaggtttagcttatgaattttgcattctttttgctgttagttccaatatctgttttagagcttgcctcatgggtgatctcaattgcctccatctaacccttaggttaaatgctttatgcagaCTAATCTCACACAATGGTCTGGAGCTAGCTTGCCTCTTCAGG
Basic information
species | Glycine max |
transcript | GLYMA17G36280.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G36280.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g08700.1 (Oryza sativa), 3'ss of exon 3
-ttggccttggtaaagttaggacatgtttgccttagtaagatgagaggtttagcttatgaattttgcattctttttgctgttagttccaatatctgttttagagcttgcctcatgggtgatctcaattgcctccatctaacccttaggttaaatgctttatgcagaCTAATCTCACACAATGGTCTGGAGCTAGCTTGCCTCTTCAGG
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gttagt-ttggtgctctgatgt--tctttatgtggggagggttatactggtctcttttaaaacttttgttattctggtaata---ttcgatgctt-ccctgctgatggaattattgttgcttttatatgtttggaggtcttactggtttcaaatgatttatgcagACCAATCTGACACAATGGACCGGAGCCAGCTTGCCACTTCAG-
upper sequence: GLYMA17G36280.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G34310.1 (Arabidopsis thaliana), 3'ss of exon 3
ttggccttggtaaagttaggacatgtttgccttagtaagatgagaggtttagcttatgaattttgcattctttttgctgttagttccaatatctgttttagagcttgcctcatgggtgatctcaattgcctccatctaacccttaggttaaatgctttatgcagaCTAATCTCACACAATGGTCTGGAGCTAGCTTGCCTCTTCAGG
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----gtatgtctgagttttagcctattt-tgtatgcatgcttata--cctactctatgaggatc-tttgtaattggttgttcgatcgatttgctgtgtacacatctgttccatg--tggcattgatagttgccattttgattctcgttgaaatatttgatacagACAAACCTCACGGAATGGTCTGGAGCTAGCTTGCCACTTCAG-
upper sequence: GLYMA17G36280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g11030.t01 (Vitis vinifera), 3'ss of exon 3
ttggccttggtaaagttaggacatgtttgccttagtaagatgagaggtttagcttatgaattttgcattctttttgctgttagttccaatatctgttttagagcttgcctcatgggtgatctcaattgcctccatctaacccttaggttaaatgctttatgcagaCTAATCTCACACAATGGTCTGGAGCTAGCTTGCCTCTTCAGG
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--------------------------------------------------------------cttcctttcttgcaacgttagttgtcttagatttgtgagaggtt-ctccatgttggttgccttgcataagcttctgacttccaa-ttaaatgtttcatgcagACAAATCTTACCCAGTGGTCTGGAGCTAGTCTGCCTCTTCTG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgggtgatctcaattgcctccatctaacccttaggttaaatgctttatgcagaCTAATCTCACACAATGGTCTGGAGCTAGCTTGCCTCTTCAGG
atctaac putative branch site (score: 2)
ttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggccttggtaaagttaggacatgtttgccttagtaagatgagaggtttagcttatgaattttgcattctttttgctgttagttccaatatctgttttagagcttgcctcatgggtgatctcaattgcctccatctaacccttaggttaaatgctttatgcagaCTAATCTCACACAATGGTCTGGAGCTAGCTTGCCTCTTCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT