Sequence
atgc intronic sequence ATGC exonic sequence...atacatacataaacatatacattgtgcttgtttttcatggttgaattttgatgtagaagtctatggaatttatttcttggtgttctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA
Basic information
species | Glycine max |
transcript | GLYMA17G05900.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g27230.1 (Oryza sativa), 3'ss of exon 4
-----atacatacataaacatatacattgtgcttgtttttcatggttgaattttgatgtagaagtctatggaatttatttcttggtgttctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA
| | ||| | | | | ||| | || | | | | | ||| | |||||| | | | ||||| || | |||||||| | ||| | ||||||||||| || ||||||||||||| ||||| || || ||||||||||| || | |||
tgcttgaatctccatgatcgaagaatttggaagcaactga-attgctagctacta--gcagatgatcatggaaagagact-taattattctctcttgct-tgcagCCGAGAGAGGTTCAGCGAGATGCATGCCAGGCTATGGTGGGAAGAAAACCGAGCGAGGATACATGAACAGTATCTCTGA
upper sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G429658_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------atacata-cataaacatat--acattgtgcttgtttttcatggttgaattttgatgtagaagtctatggaatttat--ttcttggtgtt-ctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA---------------------
|| ||| ||| | || | | || | | || | | || | | | | || | || || | | | |||| | ||||| || ||||| | |||| |||||| ||| ||||||||||||||||||| || || ||||| ||||||||| | |||
gtttgtgacccatgatgcttcagagccctttccactagcttgctcttagaataaacttgctatgtataacatgatcaacttaaaatcagagaagctagccacctacatagaattatacaagattgcagtagatacacgattgtttacatggcccttgtgct-tgcagCCGGGAGAAGTTCAGCGAGAGGCATGCCAGACTATGGTGGGAAGAGAACCGAGCGAGGATACACGAACAATACCTCTGAGAAGAAACGCCCGAGACCATC
upper sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G066672_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------atacatacataaacatatacattgtgcttgt-ttttcatggttgaattttgatgtagaagtctatggaat---ttatttcttggtgt-tctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA---------------------
| | || |||| | | | | | | |||| | | | || | | | | || | ||| || | || | |||| | ||||| || ||||| | ||||||||||| || | ||||||||||||||||| || || ||||| ||||||||| | |||
gtttgtgtccagcgctcttcccactagcttgctcttaggacaaacttgcaaggtacaagagtaacttaaaagcagagaaggcacctaagccttcactggaataggattatacaagattgcagcagatacatgattgtttacaatgtcccttgtgct-tgcagCCGGGAGAAGTTCAGCGAGATGCATGCCAGGCTGTGGTGGGAAGAGAACCGAGCGAGGATACACGAACAATACCTCTGAGAAGAGACGCCCGACACCATC
upper sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
atacatacataaacatatacattgtgcttgtttttcatggttgaattttgatgtagaagtctatggaatttatttcttggtgttctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA---------------------
||| | | |||||||| || | | || | | | ||| | | | | | ||||| || | || |||||||| | || ||||||||||| || ||||||||||||||||||||| | || || |||||||||||||||||||||
gtactgttaaacttccttacattgt-ctcaaaacccgggtttatccatcggttctgaactaaacatcactcaaact---gtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
upper sequence: GLYMA17G05900.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
atacatacataaacatatacattgtgcttgtttttcatggttga--attttgatgtagaagtctatggaatttatttcttggtgttctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA---------------------
|||| | || | | || | | ||| || | | | | || | || | | | | || || | | ||| | | ||||||||| |||||| ||||||||||||||| | |||||||| |||||||| || |||||||||||||| |||||||||
cagcatatctcaattcctgccttttacc-atttccaatagggaattacatggactttgagctgaaccccctgttcttgttt-tatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgatgtagaagtctatggaatttatttcttggtgttctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA
ttttgat putative branch site (score: 4)
tatggaatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atacatacataaacatatacattgtgcttgtttttcatggttgaattttgatgtagaagtctatggaatttatttcttggtgttctcatgtgttacatagCCGAGAAAAGTTTGGGGAGATGCATGCTAGATTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- -catacat
- - - - - - -catatac
- - - - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - -ttcatgg
- - - - - - - - - - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctatg