Sequence
atgc intronic sequence ATGC exonic sequence...cgcatacatataaggtggtcatgtgcaatatatatatatatatatatattcatattttgtttcaattcacggattctatgtcttgaattttgatgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGCGTTACTACCTCTGGGTA
Basic information
species | Glycine max |
transcript | GLYMA07G40140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40140.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G02450.1 (Arabidopsis thaliana), 3'ss of exon 1
cgcatacatataaggtggtcatgtgcaatatatatatatatatatatattcatattttgtt--tcaattcacggattctatgtcttgaattt-tg-atgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGCGTTACTACCTCTGGGTA
|| || | ||| | | ||| | ||||| | |||| | || |||| | | | | | | || | || | || | || || ||||| |||| || || || ||||| |||||||||||||||||||| |||||| |||| ||| | || || ||| | || || || || || || || || ||
---ctaattaaacaacctacatatatatcata-agatatacaaatatgtgtatgttttcataattagcttatgtatgtttaatcatagatatatgtatatgcagCTATGGCGGCGATAGGAGAGAAAGAGTGGTACTTCTATGTGCCAAGAGATCGGAAATATAGAAATGGAGATAGACCGAACCGAGTAACGACTTCAGGATA
upper sequence: GLYMA07G40140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g02020.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------cgcatacatataaggtggtcatgtgcaatatatatatatatatatatattcatattttgtttcaattcacggatt-ctatgtcttgaattttg----atgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGCGTTACTACCTCTGGGTA
| | | | | | ||| | | || | | ||| | || | |||| |||| || || | ||| || | | | ||||| |||| |||| || ||||| |||||||| |||| |||||||||||||||||| | |||||||| ||||| ||||| ||||| || || || || ||||| ||
gtacacttttctacatgaattccctcatccattttcatttcttaatttttgatgccctctctaccttcctttatttcctttttttttttttttcttttttatcatcaccatgcattcatctctcctgtatgagtagCCCTGGCTGCAATTGGAGAGAAGGAATGGTTCTTCTATGTGCCCAGAGACCGCAAGTATCGAAACGGGGATCGCCCCAACCGGGTCACCACTTCTGGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattcatattttgtttcaattcacggattctatgtcttgaattttgatgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGCGTTACTACCTCTGGGTA
ttttgat putative branch site (score: 4)
atattttgtttcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgcatacatataaggtggtcatgtgcaatatatatatatatatatatattcatattttgtttcaattcacggattctatgtcttgaattttgatgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGCGTTACTACCTCTGGGTA
-gcataca
- - - - - - - - - -catgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtc