Sequence
atgc intronic sequence ATGC exonic sequence...gcctgcccaactaacctaactaactaattcccttactaacagacacctaactaacaactaatgggtgtctactgatggacttctctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
Basic information
species | Glycine max |
transcript | GLYMA13G26610.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------------------------gc-ctgcccaactaacctaa--ctaactaattccc--ttactaacagacacctaacta------acaac-taatgggtgtctactg-----atggacttctctatttttt------tcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
|| ||| | | || ||| || | |||| | | |||| ||| ||| | ||| || | | ||||| ||| | | | || ||| |||| | ||| |||||||| || || |||||||||||||| ||||| |||||||||||| ||||| || ||||||||||||||||| | |||||
gtatctctcatctcgacgcatgattaataggatgcttaggtccggctataggagctgtcaagaactcaagatagcactgtctgcccaaactagttcttttcagttccgcataaaaaacatacatttaagaacattgtgcaatgccatagttcaatactgtttcaatgcattcgtgatgccttcaaaacatctccagGCCCAGCTTGAGAAGATTGCTCCAACTTGGATGAATATTTCGTTGAAAATGAAAGAGGATGTGGAGACAGACAAAGCTTTTGGATGGGTCTTGGAAAT
upper sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------gcctgcccaactaacctaactaactaattcccttactaacagacaccta-----actaacaactaatgggtgtctactgatggacttctctatttttttct---------tcagGATTTGA-TTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
| | | | || | | | | | | | | | || | || | ||| | || | | | | || || | ||| | ||| | ||| ||||||||||| |||||||||||| | || | | |||||||| |||| ||||| |||||||||||||||||||| | |||||
gtaacacatattgcagaattgacgtggtataccttgaagtctcatgcatgaggagtatttccttggattttatttttacattacttacatgccagttgctagttattaatgttttgaattgatgagcttcaatttttaactctatcccttatcatctgaggaaacttttagATACAACTTGAGAAGATTGCCCCTACATGGATGAATGTATCGATTCAAATGAAAGAAGATCAGGAGACAGATAAAGCTTTTGGATGGGTCTTGGAAAT
upper sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------gcctgcccaactaacctaactaac---taattcccttactaacagacacctaactaacaact--aatgggtgtctactgatggacttctctatttttt------tcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
|| | || | | | | || ||| ||| || | | || |||| | | || | | | || | | | | | |||| | ||| |||||||||||||||||||||||| | || | | |||||||||||| |||||| ||||||| ||||||||||||| | |||||
gtattttcttgttgcacacttaacacccattcacctaagcatgttattgattttctgaccattcatttggtgcattagcattcacagcctttacttcgcttgttacta--tttcggtttagtaacttcataagacctcacttcacacaatttcttttcctgtgagagcttctcagACAATTCTTGAGAAGATTGCCCCCACATGGATGAATGTGTCAATTCAAATGAAAGAGGATGAAGAGACAGATAAAGTTTTTGGATGGGTGTTGGAAAT
upper sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G055020_T03 (Zea mays), 3'ss of exon 4
-gcctgcccaactaacctaactaactaattcccttactaacagac-acctaactaacaactaatgggtgtctactgatggacttctctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
| ||| || || ||| | | | | | | | || | | | || | | ||||| || | |||| ||| | | ||| |||||||| || || ||||||||| |||| || || ||||||||||||| ||||| || ||||| || |||||||| | |||||
agataagtt--ttaatgaaatcgaccaatgctgatccaatctgtttatctgtcatgtcaatcttgactaacgtaatatggatgccttcgtaaacatctttagGCTCAGCTTGAGAAGATTGCTCCAACCTGGATGAATGTTTCATTAAAAATGAAAGAGGATCAGGAGACAGACAAAGCATTCGGATGGGTCTTGGAAAT
upper sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------gcctgcccaactaacctaactaacta--attcccttactaacagacac---ctaactaa-caactaatgggtgtctactgatg--gacttc--tctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
| | | | || ||| | || | | | | || | | | ||| | | ||||| ||| | | || ||| | | ||||| | ||| ||||||||| || |||||||||||| | || ||| |||||| | |||||||| |||||||| || |||||||||||||| |||||
gtgagattatctgtgctatactgtttgtatatgtgttatttgacttgggccccaaagattttcagaggcgtttagctagatgtgatgttggtgtccaggaatatgttctgtttgttctgttcatgcattaaaattgatgttgacatgcatttactttctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
upper sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 3
gcctgcccaactaacctaactaactaattcccttactaacagacacctaactaacaactaatgggtgtctactgatggacttctctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
| | || | | | ||| || || | | | | | |||| | | | ||| | || ||| | | ||||| ||| | | |||||||| || |||||||||||| ||||||||| |||||||| || ||||| |||||||||| ||||||||||||||||||||
atccaaaagccgcactttctttctttatttttttgctccctcatttttttttctgtaaaaatgtgaattacattttggtttacttaattgtcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAATMapped 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|192309521|gb|FG999860.1|FG999860EST: CAGTTACAAATGTTGATCCAATTGGAAATTCGCCTGTAATTATAAGAAAG GATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATG
genomic: CAGTTACAAATGTTGATCCAATTGGAAATTCGCCTGTAATTATAAGAAAGgtagaatttc ... ttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctaactaacaactaatgggtgtctactgatggacttctctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
cttctctatttttttc CT-rich tract
ttctctattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcctgcccaactaacctaactaactaattcccttactaacagacacctaactaacaactaatgggtgtctactgatggacttctctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
-cctgccc
- - - - -actaacc
- - - - - - - - - - - - - - -cccttac
- - - - - - - - - - - - - - - - - actaaca
- - - - - - - - - - - - - - - - - - - -cagacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgggtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg