Sequence
atgc intronic sequence ATGC exonic sequence...atagtaaaatacagtgtagcttttcttttccttaatgtatttggtgcttctatacaaaacttcagaattgattgtttgctccccttccactttttggcagATAAGGAGTCATGCACAGAAGTATTTCATGAAAGTTCAGAAGAATGGCACAAGTGAACATGTACCTCCCCCTCGTCCAAAGAGAAAAGCTGCTCATCCCT
Basic information
species | Glycine max |
transcript | GLYMA18G47230.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47230.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02260.t01 (Vitis vinifera), 3'ss of exon 2
------atagtaaaatacagtgtagcttttcttt-tccttaatgtatttggtgcttctatacaaaacttcagaattgattgtttgctccccttccactttttggcagATAAGGAGTCATGCACAGAAGTATTTCATGAAAGTTCAGAAGAATGGCACAAGTGAACATGTACCTCCCCCTCGTCCAAAGAGAAAAGCTGCTCATCCCT
||| || | || ||| | || | | | | ||||| ||| | | | || | | | || | | | | |||| ||||||| | || ||||| || ||||| || |||| |||||||| ||||| |||||||||||||| ||||| ||||| |||||||| ||||| || ||||| |
taatttctaggcaaccattctgcagcacgtggttatgcatggtccccactatgcttgtatg----attccc---tttcatatcttttcacatacgagatttttgcagATACGTAGCCATGCGCAAAAGTACTTTTTGAAGGTTCAGAAAAATGGTACAAGTGAACATGTGCCTCCTCCTCGGCCAAAGAGGAAAGCAGCCCATCCAT
upper sequence: GLYMA18G47230.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ36434 (Selaginella moellendorffii), 3'ss of exon 2
atagtaaaatacagtgtagcttttcttttccttaatgtatttggtgcttctatacaaaacttcagaattgattgtttgctccccttccactttttggcagATAAGGAGTCATGCACAGAAGTATTTCATGAAAGTTCAGAAGAATGGCACAAGTGAACATGTACCTCCCCCTCGTCCAAAGAGAAAAGCTGCTCATCCCT
|| || |||| | ||| || || |||| | || || | | | || || | || | ||||| || |||||||| ||||||||||| ||||||| ||||||||||| || | ||||| || ||||| || || || ||| | ||| ||||||| || |
---------------gtgaaattcctttgcttta------ttcatg-ttcttcgcggggatttagt-tcgttagtgtgtgacaatttc---------cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAGCGTAAATCTGCTCAACCAT
upper sequence: GLYMA18G47230.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ04991 (Selaginella moellendorffii), 3'ss of exon 2
atagtaaaatacagtgtagcttttcttttccttaatgtatttggtgcttctatacaaaacttcagaattgattgtttgctccccttccactttttggcagATAAGGAGTCATGCACAGAAGTATTTCATGAAAGTTCAGAAGAATGGCACAAGTGAACATGTACCTCCCCCTCGTCCAAAGAGAAAAGCTGCTCATCCCT
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---------------gtgaaattcctttgcttta------ttcatg-ttcttcgcggggatttagt-tcgttagtgtgtgacaatttc---------cagATTAGAAGTCATGCCCAGAAGTATTTTTTGAAAGTCCAGAAGAATGGAACTGGAGAACACGTTCCTCCTCCACGGCCGAAACGTAAATCTGCTCAACCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttctatacaaaacttcagaattgattgtttgctccccttccactttttggcagATAAGGAGTCATGCACAGAAGTATTTCATGAAAGTTCAGAAGAATGGCACAAGTGAACATGTACCTCCCCCTCGTCCAAAGAGAAAAGCTGCTCATCCCT
aattgat putative branch site (score: 4)
ttgtttgctccccttc CT-rich tract
tatacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagtaaaatacagtgtagcttttcttttccttaatgtatttggtgcttctatacaaaacttcagaattgattgtttgctccccttccactttttggcagATAAGGAGTCATGCACAGAAGTATTTCATGAAAGTTCAGAAGAATGGCACAAGTGAACATGTACCTCCCCCTCGTCCAAAGAGAAAAGCTGCTCATCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - -tacagtg
- - - - - - - - - - - - - - - - - - - - - - tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - caaaact