Sequence
atgc intronic sequence ATGC exonic sequence...tgtgactactaagaaaaagattgtccccttttttttatgcatggtggatcaattgtgtatttttgtcttatttgttaagatcttaattagtccctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT
Basic information
species | Glycine max |
transcript | GLYMA06G14980.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g07670.1 (Oryza sativa), 3'ss of exon 5
tgtgactactaagaaaaagattgtccccttttttttatgcatggtggatcaattgtgtatttttgtcttatttgttaagatcttaattagtcc-ctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT
|| |||| | | | | ||||| || | | || | || | || || ||| || | ||| | || | |||||||||| || || ||||||||||| ||||||||||| |||||| | || || ||| | || || ||||||||| ||| | || | |||| ||||
-gtaactatttttttgttttccttttgatcactattatggatcacaattttgtagtactctattttgttgttggtttctgtcatccttaaccagctattagATGACAAACACTATCCAGAAGAAGTTCAAGGTTTCTTCAACCCAATTATTATACCAATCTTGCCCCTATCAATCACTGACCCTCTTCCTTATTGGTCCAT
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 5
tgtgactactaagaaaaagattgtccccttttttttatgcatgg--tggatcaattgtgtatttttgtct-tatttgttaagatcttaattagtccctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT
| | | || | | || || | | | | | || | |||| | | | | ||| || || ||||| || | ||||||||||||||| || ||||||||||| ||||| ||||| || || || |||| ||| | || ||||| ||| || || ||||| || | || ||||
cattaaaaaaaaaagcggggctgctgccactaaagcagcctttaatttgagtatcagtgttctgtggcgtatataacttgagtccttaacaagcca---tcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTGTACCAATCGTGCCCATACCAAGCATTGACTTTGTTCCTCGTCGGCCCAT
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------tgtgactactaagaaa----aagattgtccccttttttttatgcat--ggtggatcaattgt--gtatttt-tgtcttatttgttaagatcttaattagtccctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT
|| | | | | || || | | | | |||| || | | | | || || | || | ||| || || ||||| || | ||||||||||||||| || ||||||||||| ||||| ||||| || || || |||| || |||| ||||| || || || ||||| | | || ||||
gtatccttttgattgtacattacccactattttttttatgtggcatatctgtcacagtatccagaaccatttgcatacaccaaactttgcatttgccactaaagcatcctgtaatttgagtattagtgttctgtggcgtataacttgagtccttaacaagcca---tcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTGTACCAGTCATGCCCATACCAGGCATTGACGTTGTTCCTTGTCGGTCCAT
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 5
---tgtgactactaagaaaaagattgtccccttttttttatgcatggtggatcaattgtgtatttttgtcttatt---tgttaagatcttaattagtccctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT
| | ||| | || || ||| || | | | || | | || | ||| || | ||||||| | | ||||||||||||||||| ||||||||||| || ||||| || || || ||| ||||||| | || ||||||||| || || | || || ||| ||||
gtatcctatgcctagcctttggtttctcattgctttattctttcacctttctatatatcttgtcttaaaccaattcgatgctgttatcttaaccaattgtacacagATGACAAATACCATCCAGAAGAAGTTCAAAGTTTCATCCACGCAGCTTCTGTATCAGTCTTGCCCATATCAAGCAATCACTCTTTTCGTCACTGGGCCAT
upper sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 6
tgtgactactaagaaaaagattgtccccttttttttatgcatggtggatcaattgtgtatttttgtcttatttg--ttaagatcttaattagtccctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT
| || | | | || ||| | | || | | |||| | ||| | | | ||||||||||||| ||| ||||| ||||||| |||||||| ||||||||||| ||||||||||| || ||||| |||||||| | ||||| |||||| || || |||| |||| ||| ||||
--aggctgcatttatgtgtttcaataactatttcctctagggcctgtctttgtgttgtaataatgtttagtcttgtttaagatcttaatcagttccttttagATGACGAATACCATCCAGAAGAAGTTCAAGGTTTCTTCAACGCAACTGCTGTATCAATCTTGTCCCTATCAAGCACTGACGCTGTTCATCTCTGGCCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatcaattgtgtatttttgtcttatttgttaagatcttaattagtccctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT
tcttaat putative branch site (score: 3)
tccctttc putative PPT
ttatttgttaagatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgactactaagaaaaagattgtccccttttttttatgcatggtggatcaattgtgtatttttgtcttatttgttaagatcttaattagtccctttcagATGACAAATACCATTCAGAAGAAGTTTAAGGTTTCTTCTACCCAACTTTTGTATCAAACATGTCCATATCAATCAGCTACCTTGTTAATCTTTGGACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
-gtgacta
- - - - - aagaaaa
- - - - - - - - - - - -tcccctt
- - - - - - - - - - - - - - - - - - - gcatggt