Sequence
atgc intronic sequence ATGC exonic sequence...tatgaatttcaccaataagataaagcgcgaaagaaagagtgtattgatagtatttctctatacatgttttattgttttctgatatcatttatttcaccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA
Basic information
species | Glycine max |
transcript | GLYMA12G36610.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G36610.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g13940.1 (Oryza sativa), 3'ss of exon 9
----------------------------------------------------------------------------------tatgaatttcaccaataagat-------aaagcgcgaaagaaagagtg--tattgatagtatttctctatacatgttttattgttttctgatatcatttatttcaccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA
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gtaaactttctttatactgatgccaaaataattacaattttaagtcatattgtagttaggattcctcagttgtgtgcgggagcctgatgttcctttatgatatctttcctactgtgcattgggatgcctgcctactgtcagagttacctggaatttttttaactaaagagttatttttcctgtt----cagTTTGTCTCTCTGACTCAACCAATCAATGCGTTAGCTTTTGTTTTTGATGGTATCAATTATGGAGCATCAGATTTTGGATATGCTGCTTATTCAATG----
upper sequence: GLYMA12G36610.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0064g00930.t01 (Vitis vinifera), 3'ss of exon 10
tatgaatttcaccaataagataaagcgcgaaagaaagagtgtattgatagtatttctctatacatgttttattgttttctgatatcatttattt----caccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA
| || | || || | || | || ||| | | | || | | ||| | | | ||| || || | || || || | |||||| | || || || ||||||||||||| || |||||||| || ||||| || |||| ||| ||||| |||||||||||| |||| || || ||
-aaaaactgttttaa-aaaacaattatcaaatcaaacattatttt--ttatgtttgctcttttttaactcattcttaactcaaatttttggctttcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG----
upper sequence: GLYMA12G36610.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0064g00940.t01 (Vitis vinifera), 3'ss of exon 11
tatgaatttcaccaataagataaagcgcgaaagaaagagtgtattgatagtatttctcta-tacatgttttattgttttctgatatcatttatttcaccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA
|| | | || | | | | || | |||| | | || | | | || | | | ||| | |||||||||| || |||||||| || ||||| |||||||||||||| || || || |||| ||| ||||| ||||||||||||||||| || || ||
--------------gtatg-tcccatatctaatatgcatttttttcttttcattttttgagctcacgatcaactgaaatatttacccttttgtgatgatagTTTGTTGCTGCAACTCAACCGATAAATTCTTTGGCCTTTGTCTTCGACGGCGTGAACTTTGGAGCATCGGATTTTGCATATTCTGCATACTCCATG----
upper sequence: GLYMA12G36610.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S88_225V6.1 (Physcomitrella patens), 3'ss of exon 10
-----tatgaatttcaccaataagataaagcgcgaaag-aaagagtgtattgatagtatttctctatacatgttttattgttttctgatatcatttatttcaccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA
|| | || || || | | || ||||| | | ||| | | || || ||| | | || | |||||||| || |||||||||||||| ||||| || |||||||||||||| | | ||||| || || || ||| | ||| |||| || || ||
tgtggcatcgcgtgtgccgatgaggtctcttatgcgagcaaagaatccagcaataagtaaatgttgtttttgagataacgtt----ggtgctgtta--cactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatagtatttctctatacatgttttattgttttctgatatcatttatttcaccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA
ttctgat putative branch site (score: 3)
tttatttc putative PPT
ttttattgttttctga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgaatttcaccaataagataaagcgcgaaagaaagagtgtattgatagtatttctctatacatgttttattgttttctgatatcatttatttcaccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA
- - - - tcaccaa
- - - - - - - - aagataaa
- - - - - - - - - - - - - - -aaagaaa