Sequence
atgc intronic sequence ATGC exonic sequence...ctgaccattttttgtttttggtcagtaacataagatattaatgtaatgttgtgagtcatatatgcatgatgaataactcaatgattggtattattttcagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTGGCTGCATGGC
Basic information
species | Glycine max |
transcript | GLYMA16G26720.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26720.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
-ctgaccattttttgtttttggtcagtaacataagatattaatgtaatgttgtgagtcatatatgcatgatgaataactcaatgattggtattatttt-cagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTGGCTGCATGGC
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tctgatgttaagttgccgctcttc--tcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
upper sequence: GLYMA16G26720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
-ctgaccattttttgtttttggtcagtaacataagatattaatgtaatgttgtgagtcatatatgcatgatgaataactcaatgattggtattattttcagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTGGCTGCATGGC
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cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttccttttta-acttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttgtgagtcatatatgcatgatgaataactcaatgattggtattattttcagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTGGCTGCATGGC
gaataac putative branch site (score: 2)
ttattttc putative PPT
attggtattatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgaccattttttgtttttggtcagtaacataagatattaatgtaatgttgtgagtcatatatgcatgatgaataactcaatgattggtattattttcagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTGGCTGCATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
ctgacca
- - - - - - - - - - - - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcaatg