Sequence
atgc intronic sequence ATGC exonic sequencegtctgtctatttttgctttactttactcgttcttatgttgctatctaatgttattattattgataccaagacttttgtactgttttattatatattatagGTTCTTAGGAAGCTTGTGGATGATGCTTCCAAGTTTTTGAACGATAAGGTTACCAAGGCTGTTGTTACTGTGCCTGCTTACTTCAATGACTCCCAAAGGA
Basic information
species | Glycine max |
transcript | GLYMA16G00410.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g14070.1 (Oryza sativa), 3'ss of exon 1
--gtctgtctatttttgctttactttactcgttcttatgttgctatctaatgttattattattgataccaagacttttgtactgttttattatatattatagGTTCTTAGGAAGCTTGTGGATGATGCTTCCAAGTTTTTGAACGATAAGGTTACCAAGGCTGTTGTTACTGTGCCTGCTTACTTCAATGACTCCCAAAGGA
||| | | | | | | || || | | || | || | | || | | | ||| ||| || | || | |||| | |||||| | ||||| ||||| || ||||||||||| || || ||||||| || || |||||||| ||||| |||||||||||||| || ||||
acacctgaatgctcagggtccataatggcataatgtagcttacattttatttacatagtaaatgg-attactaaattt-cacttttcgggtcaatgcaacagGTCTTGAGGAAGTTGGTGGACGATGCATCTAAGTTTTTGAATGACAAAATTACCAAAGCAGTGGTTACTGTTCCTGCATACTTCAATGACTCACAGAGGA
upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g03310.t01 (Vitis vinifera), 3'ss of exon 1
gtctgtctatttttgctttactttactcgtt------cttatgttgctatctaatgttattattattga--taccaagacttttgtactgttttattatatattatagGTTCTTAGGAAGCTTGTGGATGATGCTTCCAAGTTTTTGAACGATAAGGTTACCAAGGCTGTTGTTACTGTGCCTGCTTACTTCAATGACTCCCAAAGGA
|| | || | | | |||| | || || || ||| ||||||| ||||| ||| || | | || || ||| |||| ||||| || || |||||||| |||||||| || |||||| |||| ||||| || || || ||||| || || |||||||||||||||||||||||||| ||||
--ctcttcgttcctccacttttttagtgattgaaaagtttggcttattatataatgtttttatttttgggttagctaataattggtctctgtttcttat------tagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTCACAAAAGCTGTGGTCACAGTGCCTGCTTACTTCAATGACTCCCAGAGGA
upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ09963 (Selaginella moellendorffii), 3'ss of exon 2
gtctgtctatttttgctttactttactcgttcttatgttgctatctaatgttattatt-attgataccaagacttttgtactgttttattatatattatagGTTCTTAGGAAGCTTGTGGATGATGCTTCCAAGTTTTTGAACGATAAGGTTACCAAGGCTGTTGTTACTGTGCCTGCTTACTTCAATGACTCCCAAAGGA
| | | ||||| | || ||| ||||| || | |||||| |||| | | || || | ||||| | || ||||| || || || |||||||||||||||||||| || || | ||||||||| | ||||| ||||||||||||||||| ||||| || |
-----------------gtgagtaatctattcttctctt-tggtctgctgttaacgttgagtgatac----gttttttctttctcttgtt-----tggcagGTTTTGAGAAAGCTGGTCGACGACGCTTCCAAGTTTTTGAACGACAAAGTGAACAAGGCTGTCATCACTGTTCCTGCTTACTTCAATGATTCCCAGAGAA
upper sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23703 (Selaginella moellendorffii), 3'ss of exon 1
gtctgtctatttttgctttactttactcgttcttatgttgctatctaatgttattattattgataccaagacttttgtactgttttattatatattatagGTTCTTAGGAAGCTTGTGGATGATGCTTCCAAGTTTTTGAACGATAAGGTTACCAAGGCTGTTGTTACTGTGCCTGCTTACTTCAATGACTCCCAAAGGA
| | | |||||| | || ||| ||||| || | | || ||||| || || | | | | ||||| | || ||||| || || || |||||||||||||||||||| || || | ||||||||| | ||||| ||||||||||||||||| ||||| || |
-----------------gtgagtaaactgttcttctctt-tggtctgctgttaacgttgtg-----tgatacgtttgttct---ttctcttgtttggcagGTTTTGAGAAAGCTGGTCGACGACGCTTCCAAGTTTTTGAACGACAAAGTGAACAAGGCTGTCATCACTGTTCCTGCTTACTTCAATGATTCCCAGAGAAMapped 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|213599819|gb|DB968441.1|DB968441EST: ACTGCCCCGCCATTGGCAAACAGTTCGCTGCTGAGGAAATTTCTGCCCAG GTTCTTAGGAAGCTTGT
genomic: ACTGCCCCGCCATTGGCAAACAGTTCGCTGCTGAGGAAATTTCTGCCCAGgtctgtctat ... tatattatagGTTCTTAGGAAGCTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgttattattattgataccaagacttttgtactgttttattatatattatagGTTCTTAGGAAGCTTGTGGATGATGCTTCCAAGTTTTTGAACGATAAGGTTACCAAGGCTGTTGTTACTGTGCCTGCTTACTTCAATGACTCCCAAAGGA
tattgat putative branch site (score: 3)
acttttgtactgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtctatttttgctttactttactcgttcttatgttgctatctaatgttattattattgataccaagacttttgtactgttttattatatattatagGTTCTTAGGAAGCTTGTGGATGATGCTTCCAAGTTTTTGAACGATAAGGTTACCAAGGCTGTTGTTACTGTGCCTGCTTACTTCAATGACTCCCAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT