Sequence
atgc intronic sequence ATGC exonic sequence...aaagaaaacgtcaagaatcatggataaagcacattatcttataagttaattataacttaatgtggtctgttaattaataattaacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
Basic information
species | Glycine max |
transcript | GLYMA04G03970.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G03970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10970.t01 (Vitis vinifera), 3'ss of exon 1
aaagaaaacgtcaagaatcatggat--aaagcacattatcttataagttaattataacttaatgtggtctgttaattaataattaacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
| | || | |||| || || || || | ||| | | ||| ||| |||| | | |||| | | | || || ||| | |||||| |||| ||||| ||||||||| |||||||||| || || |||||||| |||||||||||||| |||||||| || |||||| | |||||||| |||
ataaaagaatgcaagtttcctgtattggaaaagcgttaaat-acaagataag-ataatggatttaggtcacattaaccacaaacaatacaatattgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGTGGTATTGTGACTGCTATGCTGACTGCTCCGGATG
upper sequence: GLYMA04G03970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g11010.t01 (Vitis vinifera), 3'ss of exon 1
--aaagaaaacgtc--aagaatcatggataaagcacattatcttataagttaattataacttaatgtggtctgttaattaataattaacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
|| || || || | || | | | ||| || || |||| | || || | ||| | ||| || || | |||||| |||| ||||| ||||||||| |||| ||||| || || |||||||| |||||||||||||||||| |||| || |||||| |||||||||| |||
cagaatgcgacctcctaatagtctctatttatatatgttactgctcaacacaag-ataatggattgaagtaa---cactaaccacaaacaatacattgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCTGACTACTTCGACGTGATTGCTGGAACAAGCACAGGAGGTCTTGTGACTGCTATGCTAACTGCTCCGGATG
upper sequence: GLYMA04G03970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10980.t01 (Vitis vinifera), 3'ss of exon 1
aaagaaaacgtcaagaatcatggataaagcacat-tatcttataagttaattataacttaatgtggtctgttaat--taataattaacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
||||| || | | || | || ||| | | | || | || |||||| | ||| ||| | ||| || || | |||| | |||| ||||| ||||||||| |||||||||| || || |||||||| |||||||||||||||||| |||| || |||||| |||||||||| |||
-aagaatgcgacctct-taatagtctctatttatatatgtcactgctcaac-acaagataatgtattaaagtaacactaaccacaaacaatacattgaatcagGCGGTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGAGGTCTTGTCACTGCTATGCTAACTGCTCCGGATG
upper sequence: GLYMA04G03970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10940.t01 (Vitis vinifera), 3'ss of exon 1
aaagaaaacgtc-aagaatcatggataaagcacattatcttataagttaattataacttaatgtggtctgttaattaataattaacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
|| | | | | || |||| | | | ||| || || |||| | || ||| | | || || | | | |||||| |||| ||||| ||||||||| |||||||||| || || |||||||| |||||||||||||| ||| |||| | |||||| |||||||||| |||
aatgcgacctcccaacaatctcgatttgtatatgttactgctcaacacaag-ataatggattgaggtaacactaaccacaaacaatacaatgttgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGGCTGCTATGCTAACTGCTCCGGATG
upper sequence: GLYMA04G03970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10880.t01 (Vitis vinifera), 3'ss of exon 1
aaagaaaacgtcaagaatcatggataaagcacattatct--tataagttaa--ttataacttaatgtggt-ctgttaattaataat-taacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
|| | |||| || | | | | || |||||| ||| | || || | || || | || ||| || | ||| || |||||| |||| ||||| ||||||||| |||||||||| || ||||||||||| |||||||||||||| ||| |||| || || ||| |||||||||| ||||
-----aatcctcaaatatgttactgtggtccaagtgtcaaatataagataaaataatggatttaggtaacactaaccacaaacaatacaatattgaatatat-cagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGATGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGACTGCCATGCTAACTGCTCCGAATG
upper sequence: GLYMA04G03970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10920.t01 (Vitis vinifera), 3'ss of exon 2
aaagaaaacgtcaagaatcatggataaagcacattatcttataagttaattataacttaatgtggt-ctgttaattaataat-taacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
|| | | | ||| ||| || | | | ||| || || | || || | || ||| || | ||| || |||||| |||| ||||| ||||| ||| |||||||||| || ||||||||||| |||||||||||||| ||| |||| || || ||| |||||||||| ||||
taatccctggctatttactgtggtccaagtgtcaaatat-aagataaaataatggatttaggtaacactaaccacaaacaatacaatattgaatatat-cagGAGCTGGATGGTGATGATGCGAGGATTGCAGACTACTTCGATGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGACTGCCATGCTAACTGCTCCGAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaattataacttaatgtggtctgttaattaataattaacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
aattaac putative branch site (score: 2)
ttaattaataattaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaagaaaacgtcaagaatcatggataaagcacattatcttataagttaattataacttaatgtggtctgttaattaataattaacgatctatacatgcagGAGTTGGACGGTGAGGATGCAAGGCTTGCAGACTATTTTGATGTGATTGCAGGAACAAGCACAGGAGGTATTGTAACAGCTATGTTAACTGCTCCAAATG
-aagaaaa
- - - - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctgtt