Sequence
atgc intronic sequence ATGC exonic sequencegtagcgattttgtggattatgttgctgtaactttttttatgcatttttgttattgtcagcaatataacctgtctccgttgttacagACTGTATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACCCAGTTTAGAAGGGATGAAAACTACG
Basic information
species | Glycine max |
transcript | GLYMA13G40080.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g74460.1 (Oryza sativa), 3'ss of exon 11
----------gtagcgattttgtggattatgttgctgtaactttttttatgcatttttgttattgtcagcaatat-aacctgtctccgttgt-tacagACTGTATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACCCAGTTTAGAAGGGATGAAAACTACG
| ||| | | || | | | | ||||| | | || |||| || || || || | | | | | |||| |||| | |||||| || ||| | | ||| |||||||||||||||| || ||| ||||| |||||||| || ||||| |||||| | || |
gtattgtattttgatttatttattaaatacaattcactgtttgttttt-catacgtatgatattttctataaaattaatattcaactgatatgcgcagATTGTACAAAGCTTATCAAAAATTGTATGCTTCCATGCATGATAAAGCAACTGGTCCACATAAAACCCAATTCAGAAGAGATGAAGATTATG
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G179732_T03 (Zea mays), 3'ss of exon 3
gtagcgattttgtggattatgttgctgtaactttttttatgcatttttg-ttattgtcagcaatataacctgtctccgttgttacagACTGTATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACCCAGTTTAGAAGGGATGAAAACTACG
||| || ||| | | | || | || || | || | || || || | | | | ||||| | | | |||| |||| | ||||||||| ||| | | |||||||||||||||||||| || ||| ||||||||||| || || ||||| ||||| | || |
gtatgaatattg------acgctactacacattcacttttacaatagtgattcttctttgtatgacaacct-----catatgtgcagATTGTACAAAGCTTACCAAAAATTGTATGCATCCATGCATGATAAAGCAACTGGTCCACACAAAACTCAATTCAGAAGAGATGAGGATTATG
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------gtagcgattttgtggattatgttgctgtaactttttttatgcatttttgttattgtcagcaatataacctgtctccgttgttacagACTGTATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCAC---ACAAAACCCAGTTTAGAAGGGATGAAAACTACG
| || || ||| || | || | || | | | | | |||||| |||||| || ||||| || ||| | || |||| | ||||||||||||||||| |||| ||| ||||||||||||| |||| | || || | | ||||| ||||||||||||||||||||||| |
gtaaaagtgttaaatctttgtgtcaacttcactggacatgagttc-tgggttcttttctgttgtctatgtcttttctgctttgttgctgtcaggaaaataacaagt-tcctcttttgcagATTATATAGAGCTTACCAGAAGCTTTATGCTTCCATGCATGATAGAGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|33388690|gb|CA851897.1|CA851897EST: ATATCTTCAGAGTTCTCATCACCGATTAACACTCCTAAGCAGCAGAAAAG ACTGTATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAAT
genomic: ATATCTTCAGAGTTCTCATCACCGATTAACACTCCTAAGCAGCAGAAAAGgtagcgattt ... gttgttacagACTGTATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttatgcatttttgttattgtcagcaatataacctgtctccgttgttacagACTGTATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACCCAGTTTAGAAGGGATGAAAACTACG
atataac putative branch site (score: 3)
tctccgtt putative PPT
atttttgttattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcgattttgtggattatgttgctgtaactttttttatgcatttttgttattgtcagcaatataacctgtctccgttgttacagACTGTATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACCCAGTTTAGAAGGGATGAAAACTACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA