Sequence
atgc intronic sequence ATGC exonic sequence...actataaatgtaaatctcacatgttaacggttaacctctggttgtgttgccaactatttttgtgatttatcttgtcccttaactgaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTACAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATCG
Basic information
species | Glycine max |
transcript | GLYMA17G16420.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 8
actataaatgtaa-atctcacatgttaacggttaacctctggttgtgttgccaactatttttgtgatttatcttgtccct-taactgaaaatgta---attgcagCTTTCATTCCAAGAATGGACACAACAAGTACAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATCG
| || || || ||| | ||| | | || | ||| ||| || || | ||||| |||| | | | || ||||| | || |||| || || ||||||||||| || ||||| ||||| || |||| || || |||||||| || |||||||| ||||||||||||||||| | |||||| |
----ttgctgaaatatttcagaaattatggagtcacattcatttggtttgttaag-ataagctagttttattttgtgcatgtttatggtgatgtaaaaactgaagCTGTCCTTTCAAGAATGGACTCAGCAAGTGCAAGAGATGCTGAATACCAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTCAAGACTGCAATTG
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G054634_T01 (Zea mays), 3'ss of exon 8
-actataaatgtaaat-ctcacatgtt----aacggttaacctctggttgtgttgccaactatttttgtgatttatcttgtcccttaactgaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTACAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATCG
| | || | | |||| | || || | || || |||| || || || | | || ||| || | | | |||| || |||| || || ||||||||||| || ||||| ||||| || |||||||||| |||||||| || |||||||| |||||||||||||| || | |||||| |
atttgtgtctgcacttgctcaagtatttttaaattatcaagtcctacttgtttttttaag-atgagtctatttcgtctggtgcatgttttaaaaac-----tgaagCTATCCTTTCAAGAATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTG
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G169080_T01 (Zea mays), 3'ss of exon 8
actataaatgtaaat-ctcacatgtt----aacggttaacctctggttgtgttgccaactatttttgtgatttatcttgtcccttaactgaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTACAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATCG
| | | | | |||| | || || | || || |||| || | || | ||||| ||||| | || | || || || | || || ||||||||||| || ||||| ||||| || |||||||||| |||||||| || |||||||| |||||||||||||| || | |||||| |
-ttgtgtctacacttgctcaagtattttgaaattatgaagtcctacttgt-ctgtttattaagataa--gtttattttgtctgatgcatgtttaaa-aactgaagTTATCCTTTCAAGAATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTG
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0012g01140.t01 (Vitis vinifera), 3'ss of exon 8
actataaatgtaaatctcacatgttaacggttaacctctggttgtgttgccaactatttt-tgtgatt-tatcttgtcccttaactgaaaatgtaat-tgcagCTTTCATTCCAAGAATGGACACAACAAGTACAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATCG
| | || | | | ||||| || | | || ||||| | | | | | | || ||| || | | || || || || |||||||||| |||||||||||||||||||| ||||| || ||||||||||| || || |||||||||||||| || |||||||||||||| | |||||| |
--ttttcatttccctttt-tatgtttgtctttgatttgtgcttgtgctcttagcagtcctacatcatgatattctgcactgacattgcaatctctatatgtagCTTTCATTTCAAGAATGGACACAACAAGTGCAAGAGATGTTGAACACAAAGAAATTCGGGGATATTGCATTTAGGGACAAGGATTTCAAGAGTGCAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgccaactatttttgtgatttatcttgtcccttaactgaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTACAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATCG
ccttaac putative branch site (score: 3)
tatttttgtgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actataaatgtaaatctcacatgttaacggttaacctctggttgtgttgccaactatttttgtgatttatcttgtcccttaactgaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTACAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATCG
- - - - - - - -ctcacat
- - - - - - - - - - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - -ccaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtg