Sequence
atgc intronic sequence ATGC exonic sequence...atgtgtgtttctgttatgtttggaaagattggcaatatattctcatcttttctattatgcttaggctaacttgttattgttattgggttaacaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
Basic information
species | Glycine max |
transcript | GLYMA17G11100.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os07g40510.1 (Oryza sativa), 3'ss of exon 12
--------atgtgtgtttctgttatgtttggaaagattggcaatatattctcatcttttctattatgcttaggctaacttgttattgttattgggttaacaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
| | || | | ||| | || || ||| | | | || | |||| | ||| | | |||| | || | | ||||||||| | | ||||| ||| ||| ||| ||||||||||||||||||||||||| ||| ||||| ||| | || ||||| | ||||| ||||||||
ctgattgagcatatcttatttctgcattttttatcatcaaca-tatgtgtttgcttgttttggtatgtt---gcttaactcttatgttgatcatgatg----ttgcagTTATCTCCACCCTCTTAACATTTGTAACAATGTTTCGGAAAGCACATGAAGAGAACCGCAAGCAAGCTGAGCTCGATAAGAAAAGGGCTGAAAAAGAGGC
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 3'ss of exon 27
--atgtgtgtttctgttatgtttggaaagattggcaatatattctcatcttttctattatgcttaggctaacttgttattgttattgggtta-acaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
|| | || || | | | || | || | | || ||| ||| | | | | || || | | | |||||||||||| || || | | |||||||||||||||| ||||||||| ||||||||| |||| ||||| || || || ||||| |||| || || || ||
gtatatatgcctcggaaacaataaacttcatcctctttagagagtggctcgttatatgtagctaataacattaagacctggtgatcgatcgatattgctgcagTTACCACGACACTCTTGAGTTTTATAAGGTTGTTTAAGAAAGCACACGAAGAGAATGTCAAGCAAGCGGACTTGGACAAGAATAAAGATGCTAAGGAAGC
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G07760.1 (Arabidopsis thaliana), 3'ss of exon 25
----------atgtgtgtttctgttatgtttggaaagattggcaatatattctcatcttttctattatgcttaggc--taacttgttattgttattgggttaacaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCA---CATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC---------------------------------------
| | | | || | || || || || | | || | || | | ||| |||| || |||| | || |||||||||| | ||||| | | |||| ||||||||||| || |||| || |||||||| |||||||||| ||||| |||||||||||||||| || || ||
gtatacgatgaacttcatcatcctcatttgtgctaatatacataaaaagtggctggctcattgtttttacgtagctaataacaatacatgattatcga--tattgcctgcagttaccgcgaccctcttgagttttgtaaggttgtttacgacagCAGCACACCAAGAGAATGTCAAACAAGCGGAGTTGGAGAAGAAGAAAGCTGCAAAGGAAGCAGAAATGGAGAAGACGAAGAAACGAGTCAGTCTCACTAA
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G07780.1 (Arabidopsis thaliana), 3'ss of exon 13
atgtgtgtttctgttatgtttggaaagattggcaatatattctcatcttttctattatgctt-aggctaacttgttattgttattg--------ggttaacaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
|||| | | || | | || ||||| | ||||| || | | | || || | || | | | |||||||||| | || || | | |||||||||||||||| ||||||||||||||||||| |||| ||||| ||||| |||||||||||||||| || |||||
-------------gtatgcctcggaaacaataaacttcatcctcatttattctaataccatagaaagtggctcattgctaataacatacatggtgatcgattgctgcagTTACCGCGACACTCTTGAGTTTTATAAGGTTGTTTAAGAAAGCACATGAAGAGAATGTCAAGCAAGCGGAGTTGGAGAAGAAGAAAGCTGCAAAGGAGGC
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 3'ss of exon 15
--------------atgtgtgtttctgttatgtttggaaa------gattggcaatatattctc-atcttttctattatgcttaggctaacttgttattg-------ttattgggttaacaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
|| | ||| | | || ||||| || | || | |||| | || | || ||| | | | |||| | ||| | | | ||||||||| | || || | || ||||||| ||||||| ||||||||| ||||||||| | |||||||| || || |||||||||||||| ||| ||
gtatggcgtaaaatatataaacttcaatcttcttaggaaatacatagaaagaaaaaaaattccctatttgttactttaagttggaattgttttgtagctaacaataattacctgatggattgctgcagTTACTATGACTCTCTTTAACTTTATAAAGTTGTTTAAGAAAGCACACGAAGAGAATGTTAAACAAGCTGACTTGGAGAAGAAGAAAGCCATGAAGCAG--
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G07760.1 (Arabidopsis thaliana), 3'ss of exon 13
atgtgtgtttctgttatgtttggaaagattggcaatatattctcatcttttctattatgcttaggctaacttgttattgttattgggttaacaattgc---agTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
| || ||| | | || | | | | | || || | || || || ||| | ||||| |||||| | ||||| || | ||||||||||||||| ||||||||| ||||||||| |||| |||| || || |||||||||||||| | || || |
gtatggcagaggaatataaatttcatcgttcctcttgtgcaattacatagaaaatggaactgttatgtagttaataacaatacctggtgacggattgctgcagTTACTGCGACCCTCCTTCACTTTATAAGGTTGTTTGAGAAAGCACACGAAGAGAATGTCAAGAAAGCTGACTTGGAGAAGAAGAAAGCCGCTAACGAAAC
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 3'ss of exon 16
------------------------atgtgtgtttctgttatgtttggaaagattggcaatatattctcatcttttctattatgcttaggctaacttgttattgttattgggtta---acaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
| | || | || | |||| | | | | || | ||| | | | | || | || |||| | || ||||||||| ||||||| | |||||||||||||||||| ||||||||| ||||||||| |||| ||||| ||| ||||||||||||||||| || || ||
gtatgacgaggaatctataaacttaaatcctcttgggcaatacatagaaaaagaaaaagtccctaatcgttatttagttggaagtgttatgtagctaataataataccgggtaatggactgctgcagTTACTGCAACCCTCTTGAATTTTATAAGGTTGTTTAAGAAAGCACACGAAGAGAATGTCAAGCAAGCGGAGCTAGAGAAGAAGAAAGCTCTTAAGGAAGC
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: AT5G07770.2 (Arabidopsis thaliana), 3'ss of exon 16
-------atgtgtgtttctgttatgtttg--gaaagattggcaatatattctcatcttttctattatgcttaggctaacttgttattgttattgggttaacaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
||| | | || | || | | ||| | | | | | || | || | || | | | | || || | | |||||||| | | || || | | |||||||||||||||| ||||||||| |||||||| |||| |||| || || |||||||||||||||| | || |
gtatacaatgaacatcatcctcatttgtgctaatacattagaagaaagtggctcattgttatgttgttgctaataagaatacatgtggtgatcgatt----gcctgcagTTAGCGCGACACTCTTGAGTTTTATAAGGTTGTTTAAGAAAGCACACCAAGAGAATGTCAAGCAAGAGGACTTGGAGAAGAAGAAAGCTGCAACGGAAGA
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 18
atgtgtgtttctgttatgtttggaaagattg-gcaatatattctcatcttttct---attatgcttaggc-taacttgttattgt---tattgggttaaca-attgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
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---------taagtcaagaactcaatgtttatgtgatccatatacattttttttttggtaatgctgaatcctaactctccatcatatttattggtgcattttgatgcagTCACTGTAACCCTCTTAAACTTTATAAGACTGTTCCGGAAAGCGCATGAAGAGAACTGCAAGCAAGCTGAATTAGAGAGGAAGAAGGCTCAGAAAGAGGTMapped 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|21256087|gb|BQ452975.1|BQ452975EST: ACTTGCACTATATTTTGGTGAGGATCCTGCTCGTTGCCCTATGGAGCAAG TTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAG
genomic: ACTTGCACTATATTTTGGTGAGGATCCTGCTCGTTGCCCTATGGAGCAAGgtaagttgat ... acaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAG
EST:
gi|192304259|gb|FG993543.1|FG993543EST: ACTTGCACTATATTTTGGTGAGGATCCTGCTCGTTGCCCTATGGAGCAAG TTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAG
genomic: ACTTGCACTATATTTTGGTGAGGATCCTGCTCGTTGCCCTATGGAGCAAGgtaagttgat ... acaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttctattatgcttaggctaacttgttattgttattgggttaacaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
ttgttattgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtgtgtttctgttatgtttggaaagattggcaatatattctcatcttttctattatgcttaggctaacttgttattgttattgggttaacaattgcagTTACCACAACCCTGCTAAATTTTATAAGGTTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - gtttctg
- - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaact