Sequence
atgc intronic sequence ATGC exonic sequence...acaagaatcaaggatatataaaccacattatatatcttatatgttaattatataacttaatgtagtctgttaacaattaacgatttatatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
Basic information
species | Glycine max |
transcript | GLYMA06G04130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G04130.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G123764_T01 (Zea mays), 3'ss of exon 1
------acaagaatcaaggatatataaaccacattatatatcttatatgttaattatataacttaatgtagtctgttaacaattaacgatttatatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
| | || || || | | ||| ||| | | ||| | || | || | || | | | || | |||| || || || | | || || ||||| || ||| | ||||| || |||||||| |||||||||||||||||||| || |||| || | ||||| ||| |||||
aatttgaattgcattcagaatg-aggagtggcatcctatttttcatacgcgaaatgctctcctgattgattcttatgtaaaactg-----ttattaattgataaagAAACTCGATGGAGAGGAAGCCAGGTTAGCAGATTACTTTGATGTCATTGCTGGAACAAGCACAGGGGGGCTTGTGACCTCAATGCTGGTTGCACCAAACA
upper sequence: GLYMA06G04130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10970.t01 (Vitis vinifera), 3'ss of exon 1
--acaagaatcaaggatatataaaccacattatatatcttatatgttaattatataacttaatgtagtc-tgttaacaattaacgatttatatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
| |||||| | | | | | | | | ||| || | |||| | | ||| ||||| | ||| || | |||| | |||||| |||| ||||| ||||||||| |||||||||| || || |||||||||||||||||||||||||||||||| || |||||||| | |||||| |||
ataaaagaatgcaagtttcctgtattggaa-aagcgttaaatacaa-gataagataatggatttaggtcacattaaccacaaacaataca-atattgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGTGGTATTGTGACTGCTATGCTGACTGCTCCGGATG
upper sequence: GLYMA06G04130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g11010.t01 (Vitis vinifera), 3'ss of exon 1
acaagaatcaaggatatataaaccaca--ttatatatcttatatgttaattatataacttaatgtagtctgttaacaatta--acgatttatatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
|| | | | || | | | |||||||| ||| || | | | | || ||||| | | ||||| | | || | ||| || | |||||| |||| ||||| ||||||||| |||| ||||| || || ||||||||||||||||||||||| ||| |||| || |||||||||| |||||| |||
-cagaatgcgacctcctaatagtctctatttatatatgttac-tgctca--acacaagataatggattgaagtaacactaaccacaaacaatacattgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCTGACTACTTCGACGTGATTGCTGGAACAAGCACAGGAGGTCTTGTGACTGCTATGCTAACTGCTCCGGATG
upper sequence: GLYMA06G04130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10980.t01 (Vitis vinifera), 3'ss of exon 1
acaagaatcaaggatat--ataaaccacatt-atatatcttatatgttaattatataacttaatgtagtctgttaacaatta--acgatttatatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
|||||| | | ||| | ||| |||||| | | || | | | | || ||||||| | ||||| | | || | ||| || | |||| | |||| ||||| ||||||||| |||||||||| || || ||||||||||||||||||||||| ||| |||| || |||||||||| |||||| |||
--aagaatgcgacctcttaatagtctctatttatatatgtcac-tgctca--acacaagataatgtattaaagtaacactaaccacaaacaatacattgaatcagGCGGTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGAGGTCTTGTCACTGCTATGCTAACTGCTCCGGATG
upper sequence: GLYMA06G04130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10940.t01 (Vitis vinifera), 3'ss of exon 1
acaagaatcaaggatatataaaccaca--ttatatatcttatatgttaatt--atataacttaatgtagtc-tgttaacaattaacgatttatatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
| | | | || | | || ||||| ||| | || | |||| | || || |||| | ||| || | || | | |||||| |||| ||||| ||||||||| |||||||||| || || ||||||||||||||||||||||||||| |||| | |||||||||| |||||| |||
----aatgcgacctcccaacaatctcgatttgtatatgttactgctcaacacaagataatggattgaggtaacactaaccacaaacaataca-atgttgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGGCTGCTATGCTAACTGCTCCGGATG
upper sequence: GLYMA06G04130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10880.t01 (Vitis vinifera), 3'ss of exon 1
acaagaatcaaggatatataaaccacattatatatcttatatgttaattatataacttaatgtagtc--tgttaacaattaacgattta----tatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
| | |||| | | | | | | | | || | | || | | | || ||| |||| | ||| || | | ||| || |||||| |||| ||||| ||||||||| |||||||||| || |||||||||||||||||||||||||||||| |||| || || ||||||| |||||| ||||
----aatcctcaaatatgtta-ctgtggtccaagtgtcaaatataagataaaataatggatttaggtaacactaaccacaaacaatacaatattgaatatat-cagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGATGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGACTGCCATGCTAACTGCTCCGAATG
upper sequence: GLYMA06G04130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10920.t01 (Vitis vinifera), 3'ss of exon 2
acaagaatcaaggatatataaaccacattatatatcttatatgttaattatataacttaatgtagtc--tgttaacaattaacgattta----tatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
|||| | ||| || | | | | | || | | || | | | || ||| |||| | ||| || | | ||| || |||||| |||| ||||| ||||| ||| |||||||||| || |||||||||||||||||||||||||||||| |||| || || ||||||| |||||| ||||
----taatccctggc-tatttactgtggtccaagtgtcaaatataagataaaataatggatttaggtaacactaaccacaaacaatacaatattgaatatat-cagGAGCTGGATGGTGATGATGCGAGGATTGCAGACTACTTCGATGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGACTGCCATGCTAACTGCTCCGAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattatataacttaatgtagtctgttaacaattaacgatttatatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
aattaac putative branch site (score: 2)
ttaacaattaacgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaagaatcaaggatatataaaccacattatatatcttatatgttaattatataacttaatgtagtctgttaacaattaacgatttatatatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCTGGAACAAGCACAGGTGGTATTGTAACAGCTATGCTAAGTGCTCCAAATG
- - - - - - - - - - aaccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctgtt