Sequence
atgc intronic sequence ATGC exonic sequence...ctttaacgttgttattcctcccaaattttggttccaaattattcaataaaatcaattgcttttcatatcattgtactaatactagaacaccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG
Basic information
species | Glycine max |
transcript | GLYMA08G43320.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G43320.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g55000.1 (Oryza sativa), 3'ss of exon 2
--ctttaacgttgttattcctcccaaattttggttccaaatt-attcaataaaatcaattgcttttcatatcattgtactaatactagaacaccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG
| | ||| | || | | | | | | | | |||| | |||| | | | | | |||||| | | ||| |||||||||||||||||| ||| | || ||||||||||| |||||||||||||| ||| | || ||||
accatcaaccatattttctgttggttaatggaatgtaatgtccagaacataaggttcattgttaccaaca--aattaactaat-caatctgcccatagtgcagATGTGCAAGTTTTTTCTCCAGCAACGATGTCGGTTTGGTAGTAACTGCCGCTTGTCCCATG
upper sequence: GLYMA08G43320.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G017923_T01 (Zea mays), 3'ss of exon 2
ctttaacgttgttat-tcctcccaaattttggttccaaattattcaataaaatcaattgct-tttcatatcattgtactaatactagaaca-ccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG
| | | | || | | || | || | ||| ||| | || | || | | |||||||| | || ||||||||| ||||||||||| |||| || ||||||||||||||||||||||| ||| | || ||||
-tctggcataattttctgcttgctaacacaaatat--aatgattggagtgtatgcgccattattatgaacaaactaactaatacaaatctggccgtagtgcagATATGCAAGTTCTTCCTACAGCAGCGATGTCGATTTGGTAGTAACTGCCGCATGTCTCATG
upper sequence: GLYMA08G43320.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g07000.t01 (Vitis vinifera), 3'ss of exon 2
ctttaacgttgttattc-ctcccaaattttggttccaaattattcaataaaatcaattgcttt--tcatatcattgtactaatactagaacaccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG
|||| || || | | || | | | | | || | | | | ||| ||| | || ||||||| ||||| |||| ||||||||| |||||||||||| |||| |||||||| |||||||| | ||||| ||| |||||||||
--ttaatgtcattggaaattttcttgttctagagcatagaaacataa-gagtcctctggttttggtcacaccaacttactaatgctagaccaccctagtgcagATATGCAAGTTCTTTCTACAGCAACGATGCCGATTTGGCACCAACTGCCGCTTATCACATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaatcaattgcttttcatatcattgtactaatactagaacaccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG
tactaat putative branch site (score: 1)
ttttcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttaacgttgttattcctcccaaattttggttccaaattattcaataaaatcaattgcttttcatatcattgtactaatactagaacaccaaagtgcagATGTGCAAGTTCTTTTTACAACAACGATGTCGATTTGGTAGTAACTGTCGCCTATCACATG
- - - - - - - ttcctcc
- - - - - - - - - - - - - - tggttcc
- - - - - - - - - - - - - - - - - - - - - - aataaaa