Sequence
atgc intronic sequence ATGC exonic sequence...tatgtcttttcacatttgtatcatattgacctgtttttccatgtagactggctgaatggattgttccctgatttctttatttcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG
Basic information
species | Glycine max |
transcript | GLYMA08G01730.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G01730.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g58750.1 (Oryza sativa), 3'ss of exon 8
tatgtcttttcacatttgtatcatattgacctgtttttccatgtagactggctgaatgg----attgttccctgatttctttatttcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG
||| | | | | | |||| ||| || ||| || | || | | || | |||| | |||| || |||| || | | |||||| ||||| || |||||||| || || ||||| || |||||||||||||||||||| || ||| ||||||||| || ||||| || |||||||||
tatacgtagttgaaactttgtcatgctgaa-tgatttagcaaccatcctcgttatattgttatgctgttgcatgatccattgttttccttgtttgct---gcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG
upper sequence: GLYMA08G01730.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 9
tatgtcttttcacatttg---tatcatattgacctgtttttccatgtagactggctgaatggattgttccctgatt-tctttatttcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG
| || || | ||||| | | || | |||||||| | |||| | || || | | || ||||||| |||| | | |||||| || || || ||||||||||| |||||||| || || ||||||||||| ||||| || ||| ||||||||| || |||||||||| |||| ||||
-acgtggattgaaatttgacgttttctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttct---gcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG
upper sequence: GLYMA08G01730.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
tatgtcttttcacatttgtatc-atattgacct-gtttttccatgtagactggctgaatggattgttccctgatttctttatt-tcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG
|| | | ||| | | || | ||| ||||| | | | | | | | || | ||| | ||||| ||| | ||||||||||||||| |||||||| ||||||||||| |||||||||||||||||||| || || || | |||||| |||||||| ||||||| | |||||||||
---gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagctatacatggtcttgctaattattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gactggctgaatggattgttccctgatttctttatttcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG
ccctgat putative branch site (score: 4)
ttccctgatttcttta CT-rich tract
tgatttctttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgtcttttcacatttgtatcatattgacctgtttttccatgtagactggctgaatggattgttccctgatttctttatttcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT