Sequence
atgc intronic sequence ATGC exonic sequence...ctttgaaatttttatagtttttcctttttcaactttatgttcgttactaagaacaagttgtatagtttaatattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG
Basic information
species | Glycine max |
transcript | GLYMA0048S00320.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g58060.2 (Oryza sativa), 3'ss of exon 5
ctttgaaatttttatagtttttc--ctttttcaactttatgttcgttactaagaacaagttgtatagtttaatattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG
| | | |||| |||| | || | || | || | | || || ||| | || | || | | | ||||||||||||||| |||| || |||| ||||| ||||| ||||| |||||||| ||||||||||| ||||||
--tctgagtcattattgtttgaaaatatatttacattagtatttttacatctttactttttttatctgcatttttttaacttacactgaattgacagtgcagGATGTTGAAGTTGAGGATAAGGTTGATGTGATAATATCAGAGTGGATGGGTTATATGCTTCTCTATGAG
upper sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g34740.1 (Oryza sativa), 3'ss of exon 5
ctttgaaatttttatagtttttcctttttcaactttatg--ttcgttactaagaacaagttgtatagtttaatattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG
|| | |||||| || || || | | |||| | | | | | |||| | | | |||| | || || |||||||| |||||||| ||| | || ||||| || || || |||||||||||||| |||||||| ||||||
--ttctatcttttattgtggttttgttactatccttataattctactttgaggtcctccttgtgttatccagtattattatattagaatatttgaaaatcagGATGTCGAAATTGAAGAAAAAGTCGATGTCATCATATCTGAATGGATGGGCTACATGCTTCTGTATGAG
upper sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G008287_T02 (Zea mays), 3'ss of exon 5
ctttgaaatttttatagtttttcctttttcaactttatgttcgttactaagaacaagttg---tatagtttaatattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG
| ||| || | | || | |||| ||| |||| | |||| || | | | | |||| | ||| || || |||||||||| |||| ||| |||| ||||||||||| |||||||||||||||||||||||||| ||||||
--tcttcattaataccgctattgtataaatgcattta-gtttgttattctatacaattttgcttttgatctgctatttcattgctgttgaactggcattgtagGATGTTGACCTTGAGGAAAAGGTTGATGTTATAATATCAGAATGGATGGGCTATATGCTTCTCTATGAG
upper sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G20020.2 (Arabidopsis thaliana), 3'ss of exon 4
--ctttgaaatttttatagtttttcctttttcaac-tttatgttcgttactaagaacaagttgtatagtttaa-tattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG
| | || |||| || | ||| | | |||||| || || | | | ||| | ||| | |||||| | || |||||||||||||| || || ||||| ||||||||||||||||| |||||||| || ||||| | ||||||
tgcaccgctcttgagatagattggttgggtgaaacatccaagttcgtatgcaaacactcctcttctgtagtaactcttcttttgttgttatgttctt----cagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG
upper sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0071g00750.t01 (Vitis vinifera), 3'ss of exon 5
----ctttgaaatttttatagtt-tttcctttttcaactttatgttcgttactaagaacaagttgtatagtttaatattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG
|||| || | || || ||||| | | | | | | | | || || ||| || | | | || || | | | |||||||||||||||||||||||| ||| ||||||||||||||||| |||||||| || ||||| || ||||||
tgtattttgttcccattgcaccagcttactctttcacttggaagctagccat--gcattgatgtgcat-gttaaacactaatcttgaattct--tgtaactgcagGATGTTGAAATTGATGAAGGGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTGCTGTATGAGMapped 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|298196408|gb|HO041151.1|HO041151EST: AAGCAAATAACTTGTCTGATGTCATTGTTGTATTGCATGGGCGAGTTGAG GATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGC
genomic: AAGCAAATAACTTGTCTGATGTCATTGTTGTATTGCATGGGCGAGTTGAGgtagactcct ... ttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGC
EST:
gi|193674616|gb|FK618212.1|FK618212EST: AAGCAAATAACTTGTCTGATGTCATTGTTGTATTGCATGGGCGAGTTGAG GATGTTGAAATTGATGAAGAGGTGGATG
genomic: AAGCAAATAACTTGTCTGATGTCATTGTTGTATTGCATGGGCGAGTTGAGgtagactcct ... ttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actaagaacaagttgtatagtttaatattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG
gtttaat putative branch site (score: 4)
tgcttttt putative PPT
ttgtatagtttaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttgaaatttttatagtttttcctttttcaactttatgttcgttactaagaacaagttgtatagtttaatattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - aagaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttatgc