Sequence
atgc intronic sequence ATGC exonic sequence...caattttttatttgcaagttcttgaatgcaggctttgcttgttttcatgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG
Basic information
species | Glycine max |
transcript | GLYMA06G18810.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 1
caattttttatttgca-agttcttgaatgcaggctttgctt--gttttcatgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG---
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-----gtgtatttggatagtttaatattttctgttcaatttaagcatcagtacatagctatgctatatcacaatgacttgacgttatgcggga-gaaacatttcagGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 2
caattttttatttgcaagttcttgaatgcaggctttgcttgttttcatgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG---
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aagttgtttgagtgacctgttcagcatacatgtcttaattgaatt-atattcattattattacccgtttctaatgttctgctggatggaaca--aaatggcagGGATACCTATAATGACCAGAGCCCAGAGAAGCCACCCTTTAGATCCATTATCTGCTGCTGAAATTGCAGTGGCTATAGCAACTGTAAGAGCTGCTGGAAA
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 1
caattttttatttgcaagttcttgaatgcaggctttgcttg---ttttcatgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG---
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----ttaccattttcaacagcctataacctagatagacacatactatttgaaatgtgtaccatgtgttaactgaactactgtttatcttgagaaa--aaaatgcagGGATACCAATAATGACAAGAGCCCAGAGGTGTCACCCTTTGGACCCATTATCTGCTGCTGAAATTGCAGTTGCTGTAGCAACTGTAAGAGTTGCTGGAAG
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 1
-------caattttttatttgcaagttcttgaatgcaggctttgcttgttttcatgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG---
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ggttgactggcctttccctttc---tgcactgttgcagatattgaatagttt-gtgctcttttgcatt-gttga-tgaattggttttgttgctatgct-ttttgcagGGATCCAGATC---ATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG
agctaac putative branch site (score: 2)
tttttaatattagcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caattttttatttgcaagttcttgaatgcaggctttgcttgttttcatgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - tgcaagt
- - - - - - - - - - - -gaatgca
- - - - - - - - - - - - - - - ggctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgta