Sequence
atgc intronic sequence ATGC exonic sequence...cattactttatactttattcaatttatttatcttactaggttttgacttttaatccattttttctaatttagcgtgcaataatcttttgtggtaaattagGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGTCTATACAAAAACAAGTTCTCATG
Basic information
species | Glycine max |
transcript | GLYMA08G26930.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G26930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g55130.4 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------------------cattacttta--tacttt--attcaatt--tatttatcttactaggttttgacttttaatccattttttctaatttagcgtgcaataatcttttgtggtaaatt---agGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGTCTATACAAAAACAAGTTCTCATG
| | || ||||| ||| ||| || ||||||| | ||| | | | | || ||||| | | || |||| ||| || ||| || |||||| ||||| ||||| | || |||||||||||||||||||||||||||||||| || || | || | | || || || ||||||| ||||||
gtaaatagcaactgtaacatgaagatagcagtagtgcttactgttttactactagtatctctctgatagtctgatgttctaatcactttggattggattgctaattatcttttaaagttactgtagctg-tagaaacatccttatttaac-tccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
upper sequence: GLYMA08G26930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 1
--cattactttatactttattcaatttatttatcttactaggttttgacttttaatccattttttctaatttagcgtgcaataatcttttgtggtaaatt---agGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGTCTATACAAAAACAAGTTCTCATG
|| ||||| | | ||| || ||||||| | ||| | | | | || ||||| | | || |||| ||| || ||| || |||||| ||||| ||||| | || |||||||||||||||||||||||||||||||| || || | || | | || || || ||||||| ||||||
ctaatcactttggattggattg---ctaattatcttttaaagttactgtagctg-tagaaacatccttatttaac-tccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
upper sequence: GLYMA08G26930.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0068g00260.t01 (Vitis vinifera), 3'ss of exon 1
cattactttatacttta-ttcaatttatttatcttactaggttttgacttttaatccattttttctaatttagcgtgcaataatcttttgtggtaaattagGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGTCTATACAAAAACAAGTTCTCATG
| || | | | | || ||| || ||| || | | | | | || || | | | | | | | | | | |||| | |||||| || || || || ||||| ||||| ||||||||||| || ||||||||||| || ||||| || ||||| || || ||| ||||||||||||||
-gctttttaaaaatcaagttggattaatatataggacccgtctcataatgtatatatatatagtatctgatggtgagacttgttttgttgtaacttgtaagGTCCTGGTTGCTCTTCTGTGGCGTATGGGGCATCTGAAGAAATAGGCCCATTTAGGATCAACAAGACTGCTTCAGGCCTGTACCTTAACAAGTTCTCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttaatccattttttctaatttagcgtgcaataatcttttgtggtaaattagGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGTCTATACAAAAACAAGTTCTCATG
ttctaat putative branch site (score: 2)
taatccattttttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattactttatactttattcaatttatttatcttactaggttttgacttttaatccattttttctaatttagcgtgcaataatcttttgtggtaaattagGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGTCTATACAAAAACAAGTTCTCATG
- - - - - - - - - - - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcgtgc