Sequence
atgc intronic sequence ATGC exonic sequence...gtatatatgagacatctatgaaaactatattatgacgctcgtttctccgcaaggctttctttttatgaggatatactaaaatttctgaggatttgtgcagGCTAAGTTGTCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATC
Basic information
species | Glycine max |
transcript | GLYMA10G42960.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 12
gtatatatgagacatctatgaaaac-tatattatgacgct-cgtttctccgcaaggctttctttttatgaggatatactaaaatttctgaggatttgtgcagGCTAAGTTGTCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATC
||| | | | | ||| || || ||| || | ||| | | || | | | | ||| | | |||| ||||| || || || || |||||||| ||||| || |||||||||||||| ||| || |||||||||||| || || ||||| | ||| || ||||
-tattgggttgttggccaagtgtttatatgttccgatgctgtgtgctgtttctgaccttgaatgatttggataaacatacacctttttctgtattt-tgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC
upper sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G16950.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatatatgagacatctatgaaaactatattatgacgctcgtttctccgcaaggctttctttttatgaggatatactaaaatttctgaggatttgtgcagGCTAAGTTGTCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATC
| ||| |||| | | || | | | || | | || | | | |||| || ||||| || || || ||| ||| ||||| || |||||| | |||||||||||||| |||||||| || ||||| | |||||| ||||| ||||||||||| |
-------------------gtaaatgttattc--atcttggtctttttgaaatgaacacaattagctaaaccctgtt----cttctaagc-----tgcagAAAAATTTATCAGCTTCTGGTGATGAGGCCTGGAAACAAAGGGAAGCTGCTGTTTTGGCTCTCGGCGCTATTGCTGAAGGCTGCATGAATGGTCTTTACC
upper sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 12
--gtatatatgagacatctatgaaaactatattatgacgctcgtttctccgcaaggctttctttttatgaggatatactaaaatttctgaggatttgtgcagGCTAAGTTGTCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATC
|| | | | | | || | || | || |||| |||| ||| || | | | ||| | | | | | |||| ||||||||||||| || || || ||||| | |||||||| ||||||||||| || || |||||||||||| ||| ||| |||||||| | |||||||||||
aaatagaagttaaaagttatatgtgtctcaaccattagtttcacttctttgcaaccatttacttgtgtttaaa-ata-tgatttccttaaaaatttctgcagGCTAAGTTATCAACTACTGATGATGAGACCTGGAAAGAAAGGGAAGCTGCCGTTTTAGCTCTTGGTGCTGTAGCTGAGGGTTGCATTACTGGTCTTTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccgcaaggctttctttttatgaggatatactaaaatttctgaggatttgtgcagGCTAAGTTGTCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATC
tactaaa putative branch site (score: 1)
atatactaaaatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatgagacatctatgaaaactatattatgacgctcgtttctccgcaaggctttctttttatgaggatatactaaaatttctgaggatttgtgcagGCTAAGTTGTCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATC
- - - - - - - -ctatgaa
- - - - - - - - - - - - - - - - - - - - - - ctccgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgag