Sequence
atgc intronic sequence ATGC exonic sequence...atgcctcatccttttgcaaatactacagaatgcaacctaagcaatattctgcttctgaatgattgatcttttattatgattttctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG
Basic information
species | Glycine max |
transcript | GLYMA13G25460.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 11
---------------------------------------atgcct---catccttttgcaaatactacagaatg--caacctaagcaatattctgcttctgaatga-------ttgatctttt--atta--tgattt-tctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG
||| | || | || || | | || |||| || | || | ||| | ||||||| | | | | ||| | | ||| | ||| ||||||||||||| |||||||||||||||||||||| ||| | ||| ||||||| |||||||| |||
gtaagtgtgcatcgcattattgttagatgctaagtaactatggttagatatgcagtttttgattcatgaagataatcaacttacctttcagatgcctaccgaaaaaactctttctgatcttgtcggtcaagtaattggtgtaatttttctttgcagATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG
upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 10
-atgcctcatccttttgcaa-atactacagaatgcaacctaagcaatattctgcttctgaatgattgatcttttattatgattttctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG
| || | | | | ||| | | | || | | | ||||||| | | || || | | | | | |||| || |||||||||||||||||| |||||||| ||||| | | ||||| || || || |||
gggactctgggagttcgtgatgctttgcttaattta-tttgattggcatgtctcatacaattgattgagtcatcaacattgttcacactttctttcg-acagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG
upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G011078_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------------------------------atgcctcatccttttgcaaatactaca------gaatgcaacctaagcaatattctgcttctg--------aatgatt--gatcttttattatgattttctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG
|| || | | ||||| |||| || ||| | || | | || ||| | | | |||| || | | | | | ||||||||||||||||||| |||| |||||||||| | || ||||| | ||| | ||||| ||||||
gtgagtgagtgagtctaccgctattattcagtctgaatccagtaaatcagaattccacaggataatagtacctatatttcctgcaaagacaaattgtacatacatcaaaagcatctcgcatggcatgttttatgtggacacgacaataactccgttcttggatgttaaaactattttgacaatctccagATCTTCTACTTCATTGGCTTTGCATTGTTCTGCCTGGAGGCTTTGCTAAGCGTGTGGGTCATTCAG
upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 9
atgcctcatccttttgcaaatactacagaatgcaacctaagcaatat-tctgcttctgaatgattgatcttttattatgattttctccatt--tgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG
|| | | ||| || | |||| || || | || | | || | | || | || |||| | |||| |||| || | |||| || |||||||||||||||||| |||||||| ||||| | || ||||||| || ||||||
ttgatcgaatatattg-ggttattcttgaat--aagtgaattcacatatttcctggtaactgctcactcatttacactatctttccacatttttgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG
upper sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 11
atgcctcatccttttgcaaatactacagaatgcaacctaag--caatattctgcttctgaatgattgatcttttatt-atgattttctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG
| ||| ||| | | | || || | | | || | ||| | | | | | ||| || ||||| | ||| || |||||||||||||||||||| |||||| ||||||| |||||| | || ||||||| ||||||||||||
aaacctaggtgacttg-accttgcatgagatacacatgagggtctctagaatatcgctggaagccttttactggattgattgatttcttctttta--ttatagATCTTCTACTTCATTGGGTTTGGAATGTTCTGTGTTGAATCAGTGCTCAGCATCTGGGTTATTCAGMapped 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|7589230|gb|AW705008.1|AW705008EST: GGGCATTCTGGCTGCCATAGATGTGCTGGGCGACCATGCTTTGATTGGG ATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGC
genomic: GGGCATTCTGGCTGCCATAGATGTGCTGGGCGACCATGCTTTGATTGGGgtaagagtgt ... tgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctgcttctgaatgattgatcttttattatgattttctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG
gattgat putative branch site (score: 4)
ttttctccatttgcct putative PPT
attgatcttttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcctcatccttttgcaaatactacagaatgcaacctaagcaatattctgcttctgaatgattgatcttttattatgattttctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG
-tgcctca
- - - - -ccttttg
- - - - - - - - - - - - - -gaatgca
- - - - - - - - - - - - - - - - - - ctaagca
- - - - - - - - - - - - - - - - - - - - - - - - ctgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatga