Sequence
atgc intronic sequence ATGC exonic sequencegtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
Basic information
species | Glycine max |
transcript | GLYMA08G02960.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 4
gtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttcca-caaaattttcttctgatgttaatgcttgctatttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
| | || | | | || ||||| | | | | | | || | ||| || || ||| || ||| || |||||||||||||||| |||||||| |||||||||||||| || |||||||| || ||| | | ||||| || |||||||||| ||| || ||||| |||||
--------------------ttttaaactaatgacatgccttttgtagttagttggtcgtcttgattatctggatagtgcactgtgattcatatttgactgaactgtctcatctcttcagGTGAGGACTTTGACCAGAGAATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 4
gtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
|| || || | | | | | | ||| | | | | | | | | | || || || | ||| | || ||| | || ||| | | || |||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||| | | ||||| || |||||||||| ||| || ||||| |||||
---------attgttgatatattt---catgcatgatctatca-gcacatttcctgtgagcttgcactgtaacttgcctatttatg--actga--gctgtatcacctcctcatt--cagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 4
gtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
| || | | ||| | | | || | || | | | | | || || || | | | || | || | |||||||||| |||||||||||||| ||||| |||||||| ||||||||||| || |||||| |||||| || |||||||||| | |||| |||| ||| |
---------------atagaattacggtggcaaatgggtgaaacccaaccaagtttttgcttctaaaatgatgatcaattgggaagtagaaaacttatgttcattttt----tctgcagGTGAGGATTTTGATCAGAGAATCATGGAATACTTCATCAAATTGATCAAGAAGAAGCATGGAAAGGACATCAGCAAGGACAACAGAGCTATTGGGAAGTT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 4
gtgagaattttttt---taatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
||||| |||||||| || ||| || | | || || | ||| | | | | || || || | ||| ||||| || | ||| |||||||||| ||||| ||||| || ||||||||||| || || ||||| || || ||||| |||||| || |||||||||| | |||| ||||| |||||
GTGAGGATTTTTTTCTCTACTGATGCTCTTTCATCTTTGCTCTTTGCACATTGAAAGAA--AATTTACGAGAGGAAAGTTATTATACTGTGGATGCTCAAGGTTCAATTCTTTCCT--GCAGGTGAGGATTTTGACCAGAGGATTATGGAGTACTTTATCAAGTTGATTAAGAAGAAGCACGGAAAGGACATCAGCAAGGACAACAGAGCTCTTGGGAAGCT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 4
gtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgct---atttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
| |||| |||| |||| || | || | ||| | | | | ||| ||||||||||||| ||||||||| | ||||| |||||||| || | ||||| || ||||| || |||||||| |||||||||| ||| || ||||| |||||
----------------------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGAAAGCT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 4
gtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgct---atttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
| |||| |||| |||| || | || | ||| | | | | ||| ||||||||||||| ||||||||| | ||||| |||||||| || | ||||| || ||||| || |||||||| |||||||||| ||| || |||||||||||
----------------------------------------------------------gtactttgatcaaagccttctccttttctttcttacagctcgaaactgacatctaccaatgcagGTGAGGACTTCGATCAGAGAGTGATGGACTACTTCATCAAGCTCATCAAGAAGAAGCACAACAAGGATATCAGCAAGGACAACCGGGCTCTTGGCAAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
tgttaat putative branch site (score: 3)
cttgctatttctcctt CT-rich tract
aaaattttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccagGTGAGGACTTTGATCAGAGAATAATGGAGTACTTCATTAAATTGATCAATAAAAAGCATAAAAAGGATATTAGCAAGGACAGCCGAGCACTTGGCAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT