Sequence
atgc intronic sequence ATGC exonic sequence...ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
Basic information
species | Glycine max |
transcript | GLYMA18G31780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 2
ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactga-atgtatgtgatg-cgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
| | |||| || || || | | | | | | | ||| || | || || || || | | | | |||| | ||||||||||||| ||||||||||| || |||||||||||||| |||||||||||||| ||||| |||| || || || || |||||||||||||| || ||
--gagagatttttttttcaaaaaaacagagaactcgagcatattagtagtacaaatccttctcaattgctgccactcttctaatgtttgtatgatctctcagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTAC
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
----ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
| || |||| ||| | | | | | | || | || ||| || || | | ||| || || | | |||||||||| || || |||||||| || |||||||| ||||| ||||||||||||||||||||| |||| || ||||| || || || |||||||| || ||
aagtgctactaacttgtcattactgaaggaaatgtataatctagc-acaacccaaaggatatttaatca--tgaagtctctaacttgttgcatttttt-tacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 2
--ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggca--ttccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
| | | | || | | | | || | | ||||| | |||| | | | | | || | | | | | | | |||||||||||| ||||||||||| || |||||||| ||||| ||||| |||||||| || || | || || || || || |||||||||||||| || ||
ttgttgtttggtagcctttattcaaagaatgaaaaca-taaaaggaacctttttgtcagtttgctctctaactgtaagttttaatcactacaattttt---tagGTAAAAGGGCATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCGAAGGCACTTGCTGCGGCTGGTGCTGAAATTCTTGTGGGTAC
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
||| | || |||| || | || | ||| | | | | | | | |||| || | | ||| ||||| ||||||||||||||| | |||||||| ||||| ||||| ||||| |||||||||||||| || || || ||||||||||| | || || ||
--------------gttggttggcatatctttctttgaa-------ttcagagaagacttggt--gctatctgaactaagcaagtgtaaatggtac--agGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
-ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
| | | || || | | | || ||| | | | | |||| | | | | | | || || | |||||| || || || ||||||||||| |||||||||||||||||||| ||||||||||| |||||||| ||||| ||||| |||||||||||||| |||||
gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaactaaaactgggat-tgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S99_59V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------ctcataaatttgttattgc-caagtgtaccttttttcttaactgtccttttttatatc--tttgatt--tgttgtggcattccactga----atgtatgtgatgcg--------cagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
| | | | | || | | || ||||| ||| | | ||| |||| | || || | ||| || | | || || ||| | | | ||| || || || ||||||||||||||||||||||| | || | ||||||||| || || ||| | || ||||||| ||||||||||| |||||||| ||
gtgtgtggcaatggcaatggtggagacggagtgaaacatggattccgtttttattatttattatttattattttaattggaatagtgtctaaacagttctgtgtgcttatttatatcgtttggagttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGGCTATTGCCAAAGCCCTGTCAGCAGCTGGAGCTGAAATCCTTGTCGGAAC
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S29_256V6.2 (Physcomitrella patens), 3'ss of exon 2
----ctcataaatttgttattgccaagtgtacctt--ttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
|| | || | | |||| | | | ||| ||| | || | || | | || | |||| | ||| | | | | | ||| ||||| || || ||||| |||||||| |||||| | || | ||||||||| || || ||| |||| |||||||| |||||||||||||||||||| ||
gtacctgacaatggcgcagcgactaagtagagcatagcttttttaggaaccgcttgctgtacc----acatgct----catttacttcaatttgtat--tttgtagGGAAAAGAGCGTTTATTGCCGGTGTGGCGGATGACCAAGGTTTTGGCTGGGCCATTGCCAAAGCTCTGGCAGCAGCTGGAGCTGAAATTCTTGTCGGAACMapped 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|15813360|gb|BI785635.1|BI785635EST: GGATTGCCAATTGATTTGAAAG GTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGG
genomic: GGATTGCCAATTGATTTGAAAGgtttacttcc ... tgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
ctttgat putative branch site (score: 5)
ttatatctttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - -tattgcc
- - - - - - - - - - -agtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgta