Sequence
atgc intronic sequence ATGC exonic sequencegtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
Basic information
species | Glycine max |
transcript | GLYMA04G38480.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 7
gtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
|||| ||| | | ||| || | | | || ||| | || |||||| | | | || | |||| |||||||| ||||||||||| ||||||| | | ||| | |||| || |||||||||||||| || ||||| |||||| |||| |||||||| ||| ||||||| | |
----------------------------------------------gtttctccaccagatttacattttcttgcctcttccgatgccatctgagcttt---gtttaattgcatatgaactcactgtgttactttcaattatttttga--agGTGATGACTGTAAACCCAGATTTTGCTACATTAGACACGACAATTCTTGATGCTCTACATATAATGCATGATGGAAAGTTCTTGCATATTCCTGTTCTTG
upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G031609_T02 (Zea mays), 3'ss of exon 7
gtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
||||| || | | || || || | || | | || ||||| ||| || | || | | || |||||| |||| |||||| || |||| | ||||| | | || |||||||| ||||||||||| ||||| |||||| |||| || ||||| ||| ||||||| | |
------------------------------------------------------------gtttctcctgcagatttatgatttgtattccaaaagatgttgaatt---ttgtattcatcctagacacacagtgtctactattttgatccagGTAATGACTGCACACCCCGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G131118_T01 (Zea mays), 3'ss of exon 5
gtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
|||||||| | | || || || ||| ||| | || | ||||| ||| || | | ||| ||||| |||| |||||| || |||| | ||||| | | || |||||||| ||||||||||| ||||| |||||| |||| || ||||| ||| ||||||| | |
------------------------------------------------------------gtttcttctgcagatttatgatt-tttattccataagtt---gttgaattttgtattcatcctagacacattgtctact-attttgatccagGTAATGACTGCACACCCCGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 7
gtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
||||| | || || || ||| | | || | | | | | | || | | | | ||| |||| |||| |||||| || |||| | ||||| | | || |||||||| ||||||||||| ||||| |||||| |||| || ||||| ||| ||||||| | |
---------------------------------------------------------------gtttcttgagatttatgattctttacttcaaaagttgttgaattttgtatttattttagacacagtgtctgttact-gttttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G177485_T01 (Zea mays), 3'ss of exon 2
gtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
|||||||| | | || || || ||| ||| | || | ||||| ||| || | | ||| ||||| |||| |||||| || |||| | ||||| | | || |||||||| ||||||||||| ||||| |||||| |||| || ||||| ||| ||||||| | |
------------------------------------------------------------gtttcttctgcagatttatgatt-tttattccataagtt---gttgaattttgtattcatcctagacacaatgtctact-attttcatccagGTAATGACTGCACACCCCGATTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
upper sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0031g02750.t01 (Vitis vinifera), 3'ss of exon 7
gtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
| | | || | | || | | | | | |||| | | ||| || || | ||| | || || | |||| | | || || |||| || ||||||||||||||||||| |||| ||| | | ||||||||||| |||||||| || || || |||||| | |||||||| |||||||||||||| || |
----------------------------cttgaaacgaga--gacctaatggatcttatagctctctcttt--gatcatgcaagttcttgtt--gtacttagcatga-------tttcacttgtgttttttccttatct-----------agGTGATGACTCCAAACCCTGAATGCGCAACCTTGGAGACAACAATCCTTGATGCGCTACACATAATGCATGACGGGAAGTTTTTACATCTTCCTGTTGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
tttgactttcttcttt CT-rich tract
aattaatttgacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG