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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

Basic information

species Zea mays
transcript GRMZM2G164352_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 8
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttga-----tgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                              | | | | ||  |||  ||   | |||  || | |||||     |    || |||  |     ||| || |        |||  |||    ||   |||         || ||||||||||| ||||| ||| ||||||| || ||| | ||||| || |||||||| || |||||| ||||||||||||| || |||||||| || || || |
------------------------------------------------------------------------------gtttg-tggc--ttaaaattgaatattcattcaggttgaccgtgtacatttcaaacacaattatttttcatatgctccctctattgaagcttgtgatttacacatgaattgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAACTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATATA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 8
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagattttttta--agttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                                   ||     |||      ||  |     ||  |   |||   |   |||    | |    |     |||| | |  || ||    | | |     | |  | || |||||||| ||||||||  || ||||||| ||  || ||||||| ||||| || ||||| ||||||||||| ||||| |||||||||||||| || || || |
-----------------------------------------------------------------------------------cttatatttaagcctttatgtccgcataccacccgatactcacaaaa----tacaaagcaaaagaaaacttttggaagacattttaatc--aatatatttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 8
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                           ||| |  |  ||| | |  ||   | | ||  || |   | | |  | |  ||    |       |||| ||||          | |||   || |  | ||   ||          |  |||| |||||||| ||||| ||  || ||||||| ||  || ||||||| ||||| || ||||| ||||||||||| ||||| |||||||||||||| || || || |
-----------------------------------------------------------ttatttaagccttatgtctgcataccaccctatact-cacaaaacatgtacaaagcaaaa-----gaaaacctt----------tgaaagacattt--taatcaatg----------tattcttgcagGTTATAGGAATCGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTCCGGCTTGCAATTATAGAATATA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 7
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                ||||  |  ||  |||  ||| ||   | || |   |  ||||    ||   | |  || |||        |  || | |  ||   |  ||| || ||  ||||            |||||     | ||  || ||||||||||| ||||| ||| ||||||| || ||| | ||||| || |||||| | || |||||| ||||||||||||| || |||||||| || || ||||
------------------------------------------------gtttgtggcttaaaattgaatattccttcagat---tgaccatgtacatttcaaacattatta--------tttttcatatgct---ccctctattgaagcttat------------gatttacacatgga--ttgcagGTTATTGGTATTGATTTGTTATCTCAGTCTCTGTTGCCAGCCATAGTAGAATTAGCTGAGGATCGGCACTGGAGAGTTCGACTTGCAATCATAGAATACA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 8
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                                 ||||    ||   ||||| |  || | |  || ||  |     | ||   |  | |  |     ||| || ||  |    || |||   |    |   |||| ||||||||||||||  | ||| ||||||||||  || ||||||| ||||| || ||||| ||||||||||| ||||| || || ||||||||||| || || |
-------------------------------------------------------------------------------agagcttatgatct-tatgccaccttctatagagatgcaga----gtaaaaatcacataacgaaaaaaacttttcaaagatatgttga---tcaagtcattcttgcagGTTATTGGAATCAATTTGTTATCTCAATCTTTGTTACCAGCCATTGTTGAGCTTGCTGAGGATAGGCATTGGAGGGTTCGACTTGCAATAATAGAATATA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 7
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaa--gccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                        |   ||       | ||    ||   |     |   ||  | |||      ||  ||| |   |||     | ||    || || ||   ||||| |    |  | || | | |  |||||| | ||   |||| |    || |  ||||||||||| |||||  | ||||| |||||  || | ||||| |||||||||||||| || ||||| |||||||||||  | ||||| ||||| ||||| |
---------------------------------------gtttgttacaacagaaatacccaaaccagatcatgccaa--tggcttcatgataacatgttttgtttaaaagactttcactcttttaacttgcctttctcgcccatccatattcagttgatgacttctatattttat----atgtggcagGTTATTGGGATTGATCTACTATCACAATCCTTGTTGCCAGCTATTGTAGAACTTGCTGAAGATAGACACTGGAGAGTAAGACTTGCTATAATCGAGTATA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 8
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtc--cttgaaagccttgcctttctcttcaaaattatc-tgatgatt-gctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
            |||  | ||     | ||| |   || ||  |  |    || | ||| || | |  ||    ||   | |   |||  | |  ||| |    ||  | ||||  ||| |  ||||| |||     |||| ||     | || || | |||||| | |  |||||  ||  |  |  ||||||||||| |||||  | ||||| |||||  | || ||||| |||||||||||||| || || |||||||||||||| || || || ||||| ||||| |
-----------gtttgctattgaccaagttactcatctctttgta-cgacattgggtttctattttt-tcccacatgttcaaaggagctgt-atcatgtt----ttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAACTTGCTGAAGACAGGCACTGGAGAGTACGTCTGGCTATAATCGAGTATA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 8
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                                             || || |  || | | |   |   ||   | || |    |    ||   | |  | |||  || |||   |||| || | ||||       |||||||||||||||||  | |||||||||||  || |||| || |||||||||||||| |||||| |||||||||||||||| ||||||||||| |||||  
---------------------------------------------------------------------------------------------gtttgttgcatctctct---tgtgtgctttagatactacttttattgcttccttatttagttggtga---ctgaattatctttta---cggcagGTTATTGGAATTGATCTACTATCTCAATCCTTGTTACCGGCCATTGTAGAACTTGCTGAGGATCGGCACTGGAGAGTCCGACTTGCAATAATAGAGTATG

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 9
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                                                                  ||      |    |    |   ||||  | |      ||||  |||    | |  || || | |   ||   | ||   |  | ||   | ||||     ||||||| |||||||||||  |||| ||||||||  | || || || ||||| || ||||| |||||||| |||||||| || |||||||||||||| || ||||
----------------------------------------------------------------------------------gcccaaattctacaaatgaatcttttccatggctgaatcctgaaaaa---tacaattttcattagtgttcagt-atttcttttcatgcatattttt-ctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA

Mapped 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|87156353|gb|DY401142.1|DY401142
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|67016540|gb|CO445289.1|CO445289
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|87157118|gb|DY401907.1|DY401907
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|31362531|gb|CD446888.1|CD446888
EST:     CTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: CTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|26558526|gb|CA830761.1|CA830761
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|67017790|gb|CO446539.1|CO446539
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|32933390|gb|CF038202.1|CF038202
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|22546073|gb|BU098394.1|BU098394
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|42491785|gb|CK700831.1|CK700831
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|23357737|gb|BU645386.1|BU645386
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|67022121|gb|CO450870.1|CO450870
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|211315613|gb|FL415838.1|FL415838
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCARGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|26560084|gb|CA832319.1|CA832319
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|67039515|gb|CO465770.1|CO465770
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|13315895|gb|BG410243.1|BG410243
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
                                               tctttc  CT-rich tract
                                  atttttgttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA