Sequence
atgc intronic sequence ATGC exonic sequence...gcaaccaacatgaatttattaataatgtacctgaaatatgtcatatgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctgcagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG
Basic information
species | Glycine max |
transcript | GLYMA02G48050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 3'ss of exon 4
---gcaa-ccaacatgaatttattaataatgtacctgaaatat-gtcatatgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctg-cagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG
| | ||| |||| || ||||| || | || || || |||| || | |||| | | | || | || || || | ||||||||||||||||| || |||||| | | || ||||| || ||||||||||| | |||||||| |||||||||||||| || ||||
tatgtgatccattatgacaccatgttccatgtaactccgtggtagttatgtg-tatt-ctgttgttccatatgcataactatgaccatc----ttctgcttttcagATAATTGATGCTGTTGTTGCTGCACGTATCTTAAATGCCACACTTGTTGTTCCCAAATTGGATCAAACATCTTTCTGGAAAGATGCAAG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 7
---gcaaccaacatgaatttattaataatgtacctgaaatatgtcatatgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctgcagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG
| ||| | || || || || || | | | | | || | | |||| ||| || | | | | | | ||||| |||||||||| || |||||| |||| ||||| || ||||||||||| || |||||||| | |||||||||||| || ||||
agcattgcagtaatgccatggttctacatttatttggaac-tcttaagtagttatgttttttttccatatt-agatatatcatgacatctgct-tatttctagATAGTTGATGCTGTTGTCGCTGCACGCATTTTAAATGCAACGCTTGTTGTTCCCGAATTGGATCAAAGATCTTTCTGGAAAGATTCAAG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168614_T02 (Zea mays), 3'ss of exon 4
gcaaccaacatgaatttattaat------aatgtacctgaaatatgtca-tatgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctgcagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG
|||| || ||||| | || | | |||| | || | || | | |||| ||||| | | || || ||||| |||||||||| || |||||| | | ||||||||||| ||||||||||| | ||||||| |||||||||||||| || ||||
------cttatgagttatttaatccgttctgaggactaaagtttagtcactgaacttatttgcttgctttctctatagacgaattataacccctgctgct-ctctagATAGTTGATGCTGTAGTTGCTGCACGTATATTGAATGCTACACTTGTTGTTCCCAAACTGGATCAAACATCTTTCTGGAAAGATTCAAG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168614_T03 (Zea mays), 3'ss of exon 4
gcaaccaacatgaatttattaata------atgtacctgaaatatgtca-tatgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctgcagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG-----------
|||| || ||||| | || | | |||| | || | || | | |||| ||||| | | || || ||||| |||||||||| || |||||| | | ||||||||||| ||||||||||| | ||||||| |||||||||||||| || ||||
------cttatgagttatttaatccgttctgaggactaaagtttagtcactgaacttatttgcttgctttctctatagacgaattataacccctgctgct-ctctagATAGTTGATGCTGTAGTTGCTGCACGTATATTGAATGCTACACTTGTTGTTCCCAAACTGGATCAAACATCTTTCTGGAAAGATTCAAGGTATGCGATAG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g03240.t01 (Vitis vinifera), 3'ss of exon 4
gcaaccaacatgaatttatt-aataatgtacctgaa-atatgtcatatgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctgcagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG
|| | || || | || ||||| | ||| | || || | | || | || | | ||| | ||||||||||||| ||||| || || || || | |||||||||| |||||||||||||| ||||||| || | |||||| |||||||| | ||
acatacttcactcatcattagaacaatgtggaggtttataatggttgtgttactaatttagttttttatcctgagta--tgttatatccatcatggctgcagATAACAGATGCAGTTGTTGCAGCTCGTATTTTGAATGCCACTCTTGTTGTTCCCAAGTTGGACCAGAAATCTTTTTGGAAGGATAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctgcagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG
aattaat putative branch site (score: 3)
aattaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaccaacatgaatttattaataatgtacctgaaatatgtcatatgctattgctctaaatccaaggagagaccaattaatatgggagttgtggctgcagATAATTGATGCTGTGGTGGCTGCATATCTTTTGAATGCTACTCTTGTTGTTCCAGAGTTGGATCATACATCTTTCTGGAAGGACACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
-caaccaa
- - - - catgaat
- - - - - - - - - - - -aatgtac
- - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaagga