Sequence
atgc intronic sequence ATGC exonic sequence...tttatttcagtgccatgttggagggagttacattttgcaaacacaatacaattcctctctgcactttactctgattgttgttgtttggttttgggaacagGTTGATGGGAAAGGTTACATCTGATAAGTGCCACAAATGGGTCTTCAAAGAGCCTACGGAATGTGAGCCTAATATCTCCAACTACTGGCAGAGTTCCTTT
Basic information
species | Glycine max |
transcript | GLYMA06G36190.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g25920.1 (Oryza sativa), 3'ss of exon 3
--tttatttcagtgccatgttggagggagttac-attttgcaaacacaatacaattcctctctgcactttactctgattgttgttgtttggttttgggaacagGTTGATGGGAAAGGTTACATCTGATAAGTGCCACAAATGGGTCTTCAAAGAGCCTACGGAATGTGAGCCTAATATCTCCAACTACTGGCAGAGTTCCTTT
| || | | | | | | || | | || | | ||| |||| | || | ||| || |||| ||||||||||||| | |||||||| || ||||||||||||||||| || ||| | ||||| ||||| || ||| |||||||||||||||| || |||
tggtcgctttcactttgttctactactactaccgagcttttgagcgtgatgttggtaagacgatgattttgatctgg--accgctggtgggtgctgctg-cagGCTGATGGGAAAGGTGGCGTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCGCCAACTACTGGCAGAGCTCTTTT
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G302293_T01 (Zea mays), 3'ss of exon 3
tttatttcagtgccatgttggagggagttacattttgca----aacacaatacaattcctctctgcactttactctgattgttgttgtttggttttgggaacagGTTGATGGGAAAGGTTACATCTGATAAGTGCCACAAATGGGTCTTCAAAGAGCCTACGGAATGTGAGCCTAATATCTCCAACTACTGGCAGAGTTCCTTT
||||| | | ||| | | | | || | || || | | | | | ||||| || | | | |||| ||||||||||||| | |||||||| || ||||||||||||||||| || ||| | ||||| ||||| || |||||||||||||||||||| |||||
---atttcggaggcatacaatacatacatgagtcatggacgataatgtgctaatagacagacccatgggtccgtttgatttggaccgtc-gctcccgcatgcagGCTGATGGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCCTTC
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G132251_T01 (Zea mays), 3'ss of exon 3
tttatttcagtgccatgttggagggagttacattttgcaaacacaatacaattcct--ctctgcactttactctgattgttgttgtttggttttgggaacagGTTGATGGGAAAGGTTACATCTGATAAGTGCCACAAATGGGTCTTCAAAGAGCCTACGGAATGTGAGCCTAATATCTCCAACTACTGGCAGAGTTCCTTT
|| | | |||| | || | | | | | | | |||| || | | | | | || |||| ||||||||||||| | |||||||| || ||||||||||||||||| || ||| | ||||| ||||| || |||||||||||||||||||| || ||
--agcttttggggcatgcaaacgcatgtgaatcatgaatgatgtgctcaagaccgtgggtctgattttgggttttggacccccttctccttcctgcatgcagGCTGATGGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCTTTC
upper sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------tttatttcagtgccatgttggagg-----gagttacattttgcaaacacaatacaattcctc-tctgcactttactctgattgttgttgtttggttttgggaacagGTTGATGGGAAAGGTTACATCTGATAAGTGCCACAAATGGGTCTTCAAAGAGCCTACGGAATGTGAGCCTAATATCTCCAACTACTGGCAGAGTTCCTTT
| | | ||| | | ||| | ||| | | | ||| | || |||| || ||| || | || |||| | | ||| |||| || |||||||||||| |||||| ||||||||||||| || |||||||| |||||||||||| | || ||||| || ||| |||||||||||||||||||||| |||
gtgggtactgggtaggtgtttttatttgatttcatctctctctccctctctttccctctctccctcattccctccctctctctctctcaacaatagggaggaagcagaaaagtgaaaaaataaaaataaaaaacaaaaattcctctaca-tgggctttgatagg-atgaattgcttttatgagcagGTTGATGGGGAAGGTTGCATCTGATAAGTGTCATAAATGGGTTTTCAAAGAGCCTTCAGAGTGTGAACCAAATGTCTCCAACTACTGGCAGAGTTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacaattcctctctgcactttactctgattgttgttgtttggttttgggaacagGTTGATGGGAAAGGTTACATCTGATAAGTGCCACAAATGGGTCTTCAAAGAGCCTACGGAATGTGAGCCTAATATCTCCAACTACTGGCAGAGTTCCTTT
ctctgat putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatttcagtgccatgttggagggagttacattttgcaaacacaatacaattcctctctgcactttactctgattgttgttgtttggttttgggaacagGTTGATGGGAAAGGTTACATCTGATAAGTGCCACAAATGGGTCTTCAAAGAGCCTACGGAATGTGAGCCTAATATCTCCAACTACTGGCAGAGTTCCTTT
- - - tcagtgc
- - - - - - - - - tggaggg
- - - - - - - - - - - - - - - - - - -caaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgttg