Sequence
atgc intronic sequence ATGC exonic sequence...taatggatttatttaaataagcctttcatactaaatcacattaagtacttcttttcccattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
Basic information
species | Glycine max |
transcript | GLYMA18G43020.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
---taatggatttatttaaataagcctttcatactaaatcacattaagtacttcttttcccattcttgata--tttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
|| | || | || | | | || || |||| | | || || ||| || | | ||| || | | | | | ||||| | ||||||||||||||||||| ||||| || |||||||| ||||||||||| |||||| | ||||| ||||| ||||| || || |||||||| ||||| |||
ctgtactagaaacaatt---tgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaactttcctattcctgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 4
taatggatttatttaaataagcctttcatactaaatcacatta--agtacttcttttcccattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
| | || | || ||| | | |||| | | | |||| ||||| ||| | | | || | | || |||||||||||||||| || |||||||| |||||||| ||||||||||| |||||| ||||||||||||| ||||| || || |||||||| ||||| |||
-ttcgcctgccatttagtactcctgtaacttgtcatcatgctgtcatcaattctgcattttttcttt-cattctgctaactataccttattctttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGGCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 2
taatggatttat--ttaaataagcctttcatactaaatcacatta-agtacttcttttcccattcttgatatttaacca-ttgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
| | | || | || || | | || || | | | |||| || | ||| | | | | | || || | |||||||||||||||| || |||||||| |||||||| ||||||||||| |||||| |||| |||||||| ||||| || || |||||||| ||||| |||
--gctcacctgtcatttagtactgctataacctgtaaccatgctgtaatcgttctgcaattttttctttcattctgctaactataccttttctttttggt--agATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGTCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------------------taatggatttatttaaataagc-ctttcata-ctaaatcacattaagtactt----cttttcccattctt-----gatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
| || || | | || | | |||| || || ||| | |||| | ||| | ||| | | | | |||| || | | | ||||||||||||||||||||||||| || || || || || ||||| | |||| || |||| |||||||||||||||||||| ||||||||||| |||
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagacttttggtagctgtgattttttgctttcctctaaagattctgagaaactcttttatctcaaat-gttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
taatggatttatttaaataagcctttcatactaaatcacattaagtacttcttttcccattcttgatatttaaccattgttt--tctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
||| || || || || || | || | || | | || | | | || | | | | || |||| | | || ||||||||||||||||||||||||| ||||| |||||||||||||| | |||| || |||| |||||||||||||||||||| ||||| ||||| |||
-gcaagatataattctgtat-ccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataactaattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG
upper sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
-taatggatttatttaaataagcctttcatactaaatc-acattaagtacttcttttcccattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
|| | | | | ||| || | || ||| ||| | | ||| | | |||| | || | | ||||| |||||||||||||| || ||||||||||| ||| | ||||| ||||||||||||||||| ||||||||||| |||||||||||||| || |||||||||||||||
gagataggataaaattggaaag--ttatgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttcttttcccattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
ttctcac putative branch site (score: 2)
ttttctcactgttc CT-rich tract
attcttgatatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatggatttatttaaataagcctttcatactaaatcacattaagtacttcttttcccattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - -cctttca
- - - - - - - - - - - - - - - - -aatcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcactg