Sequence
atgc intronic sequence ATGC exonic sequence...tttcaaatacatctacaattgttgtcatgatgacagttttgctaagtattttgttgatgatgccaagaatcttgatcattatctggtgcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCGGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
Basic information
species | Glycine max |
transcript | GLYMA06G22870.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g49570.1 (Oryza sativa), 3'ss of exon 8
tttcaaatacatctacaattgtt-gtcatgatgacagttttgctaagtattttgttgatgatgccaagaatcttgatcattatctggtgcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCGGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
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--------------------gtaagttatgcttcagatttcaccaatttattagcagcagagtttcgttatgt--attggttgttgttatttgaact--agGATGTGGCGGGAAATTCGACTCCTAGCTGACACCAAGCCTGTGGTTGCTTCAATGTCTGATGTTGCTGCAAGTGGTGGGTACTACATGGCAATGGCTGCA
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G122843_T02 (Zea mays), 3'ss of exon 13
tttcaaatacatctacaattgttgtcatgatgacagttttgctaagtattttgttgatgatgccaagaatcttgatcattatctggtgcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCGGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
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-gtaagttacgccttaggatttagtgat--ttgcttctcagcagcagcagcagcagagttttttcagtaacat-attacgaattcttatttcaact--agGATGTGGAGAGAAATCCGACTTCTAGCCAACTCTAAACCTGTAGTTGCTTCGATGTCTGATGTTGCTGCAAGTGGGGGCTACTACATGGCAATGGCTGCA
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 8
tttcaaatacatctacaattgttgtcatgatgacagttttgctaagta-ttttgttgatgatgccaagaatcttgatcattatc-tggtgcatgatc---tgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCGGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
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-----tatctatctagcctagaggtcatgtgtggatttgaatttaatagctttggaaatccttctaggctttattataatcttcattattcataatggtatacagAATGTGGAGGGAGATCAAACTACTGGCTGAAACAAAACCCGTCATTGCGTCAATGTCAGATGTGGCAGCAAGTGGAGGCTACTACATGGCAATGGCTGCA
upper sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 4
----tttcaaatacatctacaattgttgtcatgatgacagttttgctaagtattttgttgatgatgccaagaatcttgatcattatctggtgcatgatc-tgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCGGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
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gcttgtacagatgaaaaaagagaaggaatgagaaaagaaaaatgcatgacaaatataatga-gctcccactaa--ttggtccttaatt--tttatgattatgcagAATGTGGAGGGAAATCAGACTTCTGGCTGCCTCAAAACCTGTCATTGCATCAATGTCTGATGTGGCTGCTAGCGGAGGGTACTACATGGCAATGGGAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattttgttgatgatgccaagaatcttgatcattatctggtgcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCGGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
tcttgat putative branch site (score: 4)
atcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcaaatacatctacaattgttgtcatgatgacagttttgctaagtattttgttgatgatgccaagaatcttgatcattatctggtgcatgatctgcagGATGTGGAGAGAAATCCGGCTTTTGGCTGCTTCAAAACCGGTCATTGCTTCAATGTCTGATGTGGCAGCAAGTGGAGGGTACTACATGGCAATGGGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - -tgttgtc
- - - - - - - - - - - - - -tgatgac
- - - - - - - - - - - - - - - - - - - -tgctaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtgc