Sequence
atgc intronic sequence ATGC exonic sequence...ttactgccattttttatttccttcaagggaattcaatgtcttttcagtttgctttatttttattttgctgatctttatgagagacatgcatataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
Basic information
species | Glycine max |
transcript | GLYMA02G39360.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
------ttactgccattttttatttccttcaagggaattcaatgtcttttcagtttgctttattt--ttattttg-ctgatctttatgagagacatgca---tataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
| || | || | | | | || | || | || || | || | ||| | | | | || || ||| || || |||| | | | |||| ||||| ||||| || || ||||||||| || || || || || || || ||||||||||| || |||||||| || ||||||||||||||||| |
gtaaaatgggtgttaagttgtttgttgattgcacatat-cgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
ttactgccattttttatttcct--tcaagggaat---tcaatgtcttttcagtttgctttattt--ttattttg-ctgatctttatgagagacatgca---tataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
|| | || | || | | | | | || || | || || | || | ||| | | | | || || ||| || || |||| | | | |||| ||||| ||||| || || ||||||||| || || || || || || || ||||||||||| || |||||||| || ||||||||||||||||| |
gtaaaatgggtcttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
ttactgccattttttatttccttcaagggaattcaatgtctttt--cagtttgctttatttttattttgctgatctttatgagagacatgca---tataacgca--gACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
|| | | | || | || || | ||| |||| | || | || | ||| | ||| | ||| || | || | | | | | | ||| ||||| ||||| || ||| ||||||||| ||||| ||||| || || || ||||||||||| || |||||||| |||||||| |||||||| || |
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatt-tatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
ttactgccattttttatttccttcaagggaattcaatgtcttttcagtttgc-tttatttttattttgctgatctttatgagagacatgca-tataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC-----------------
|| ||| | || | || | | ||| | | ||| | |||| | | | | |||| ||||| ||||| || ||| ||||||||| || || || || || || || ||||||||||| ||||||||||| |||||||| ||||||||||| |
--------------------------------------------caatttacattcacttatgtattgat--tgtttgctaagtgtgtgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
ttactgccattttttatttcct--tcaagggaattca--atgtcttttcagtttgc-tttatttttattttgctgatctttatgagagacatgca-tataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
|| ||| | ||| | | | ||| | | || || || ||| | || | || | | ||| | | ||| | |||| | | | | |||| ||||| ||||| || ||| ||||||||| || || || || || || || ||||||||||| || |||||||| |||||||| |||||||||| |
----tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggt--tgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
ttactgccattttttatttccttcaagggaattcaatgtcttttcagtttgc-tttatttttattttgctgatctttatgagagacatgcatataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
|| | ||| || || |||| ||| || |||| ||| || ||||| | | | ||| | ||| | | | |||| |||||||||||||| ||| ||||||||| ||||||||| || ||||| || |||||||||||||||||||||||||||||||| || || || ||||
-acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttgctttatttttattttgctgatctttatgagagacatgcatataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
atataac putative branch site (score: 3)
tttatttttattttgc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttactgccattttttatttccttcaagggaattcaatgtcttttcagtttgctttatttttattttgctgatctttatgagagacatgcatataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- -ctgccat
- - - - - - - - - tccttca
- - - - - - - - - - - - - - - - -caatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca