Sequence
atgc intronic sequence ATGC exonic sequence...acaaatgttgcattctctcttcacacagcagttctttatcattcttttttttaaaatagattctggatccatgttcctgataatggtcttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCCCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTAGTGCTG
Basic information
species | Glycine max |
transcript | GLYMA16G06580.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G06580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g55010.1 (Oryza sativa), 3'ss of exon 5
------------acaaatgttgcattctctcttcacacagcagttctttatcattcttttttttaaaatagattctggatccatgttcctgataatggtcttccattct-cagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCCCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTAGTGCTG
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tatcctcgagtataaaatttcacacgcataattcacatattagatca--accaactcttattttaatccaccttatgtg-----------gaaaatgcctttccattctgcagGATCCAGTCCAAAGTAGTGTAACTGTTGGAGTTTCGCACTTTGAGAGATGCTCCCTCTGGGTTCAAGTCTTGTATTACCCATTTTATGGAAGTGGAGGGT
upper sequence: GLYMA16G06580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G472770_T02 (Zea mays), 3'ss of exon 3
acaaatgttgcattctctcttcacacagcagttctttatcattcttttttttaaaatagattctggatccatgttcctgataatggtcttcca--ttctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCCCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTAGTGCTG
|||| ||| | | | || | | || | | | | | || || | |||| | | ||| | || | ||||||||||| | |||||||| ||||| ||||| || ||||| ||||| | || ||||||||||| ||||||||||| || ||||| |||||||
--aaatattggtctatttacaaactaaaaacttactatagaattgtatgcttggggtaaacactggcattactgatcacctaacgcctttttaaccctccagGATCCAGTCCAAAGTAGTGTGACTGTTGGAGTTTCACATTTTGAGAGATGCTCGCTCTGGGTTCAAGTTTTGTATTACCCGTTTTATGGAAGTAGTGGAT
upper sequence: GLYMA16G06580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G060727_T03 (Zea mays), 3'ss of exon 2
-acaaatgttgcattctctcttcacac-agcagttctttatcattcttttttttaaaatagattctggatccatgttcctgataatggtcttcca--ttctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCCCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTAGTGCTG
|||||| ||| ||| | | || || | | || | | | | || || | | ||| || | ||||| | || | | |||||||| || | |||||||| ||||| ||||| || ||||| ||||| | || ||||||||||| ||||||||||| || ||||| ||| |||
aacaaatattgg--tctatttacaaactaaaaactcactgtagaattatgctt--gggtaaactttggcattattgatcacctaatgcttttttatatctccagGATCCTGTCCAAAGTAGTGTGACTGTTGGAGTTTCACATTTTGAGAGATGCTCGCTCTGGGTTCAAGTTTTGTATTACCCGTTTTATGGAAGTGGTGGAT
upper sequence: GLYMA16G06580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0171g00280.t01 (Vitis vinifera), 3'ss of exon 5
acaaatgttgcattctctcttcacacagcagtt--ctttatcattcttttttttaaaatagattctggatccatgttcctgataatggtcttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCCCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTAGTGCTG
| || | || |||| ||| || |||| | ||| || || | | || | | ||| | || | || ||||||||||| | ||||||||||| |||||||| ||||| ||||| |||||||||||||||||||| || | ||||| || |||||||| || ||| ||
--agattccatttgctttcttgttttggcattttcctttgtaatttttacgttgtactttcatgataagatcttgtgatccgtcatctgttcttgttgctagGATCCAGTGCTCTGCAGTGTGACCGTTGGTGTGTCCCATTTTGAGAGATGTGCCCTTTGGGTTCAGGTCCTATATTATCCCTTCTATGGGAGCGGTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttaaaatagattctggatccatgttcctgataatggtcttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCCCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTAGTGCTG
tcctgat putative branch site (score: 3)
tcttccattctc putative PPT
ttaaaatagattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaaatgttgcattctctcttcacacagcagttctttatcattcttttttttaaaatagattctggatccatgttcctgataatggtcttccattctcagGATCCAGTGTTGTGCAGTGTGACAGTTGGTGTTTCCCACTTTGAAAGATGTGCCCTTTGGGTTCAAGTATTGTATTACCCATTCTATGGTAGTAGTGCTG
- - - - -gcattct
- - - - - - - - - - -cacacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttc