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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATTATTCGGTGCGGAGGCCCCGTTGAGGATGATATGGCCAACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacgaacgggacaaccgtttgctgctgtaattcccatgtgaatagaacatgcttgcgctttaaataaacctttgtttgttgataccagacagtga...

Basic information

species Zea mays
transcript GRMZM2G121456_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121456_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 5'ss of exon 4
AGAATTATTCGGTGCGGAGGCCCCGTTGAGGATGATATGGCCAACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacgaacgggacaaccgtttgctgc-tgtaattcccatgtg----aatagaacatgcttgcgctttaa-ataaac--ctttgtttgttgataccagacagtga
|| ||||| ||||| || || ||||| |||||||||||||| |||||||| || || || ||||| || ||||| || || ||||| || |||||||||| ||     |  ||  | | |  | |  |||||| || |     |  |  |  |||    |||||   |  |||  |||  | |    ||||          
AGGATTATCCGGTGTGGTGGACCCGTGGAGGATGATATGGCGAACATCATCGTTGCCCAGCTGCTATATCTCGATGCCATCGATCCTAACAAGgtgaaaatgatgaataagacgctatccgacatccaattcctatttcctataccaatagctgccaaagctttgttacgaactgcttactctaaaaatactg--------
















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|110519563|gb|EE023896.1|EE023896
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|211481382|gb|FL023994.1|FL023994
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTGGAATG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTGGAATG
EST: gi|74237088|gb|DT645002.1|DT645002
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|78092088|gb|DV520462.1|DV520462
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|211481381|gb|FL023993.1|FL023993
EST:     CATCATTGTAGCACAGCTGCTCTACCTCGACGCTATTGATCCCCAATAAG                         GATATCATTATGT
genomic: CATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCC-AATAAGgtgaaaacga ... cttcctgtagGATATCATTATGT
EST: gi|19821991|gb|BQ048015.1|BQ048015
EST:     ACATCATTGTAGCACAGCTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|71436538|gb|DR817588.1|DR817588
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|148939986|gb|EC884717.2|EC884717
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|61119391|gb|DN560352.1|DN560352
EST:     ACATCATTGTAGCACAGCTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGT
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGT
EST: gi|211478511|gb|FL023987.1|FL023987
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|32913968|gb|CF018780.1|CF018780
EST:     ACATCATTGTAGCACAGCTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTGGAAT
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTGGAAT
EST: gi|26456147|gb|CA827730.1|CA827730
EST:     CGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: CGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|149088221|gb|EE177331.2|EE177331
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|101399114|gb|EB821430.1|EB821430
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|78111070|gb|DV529467.1|DV529467
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|78544613|gb|DV622111.1|DV622111
EST:     ACATCATTGTAGCACAGCTGTTCTACCTGGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|76919121|gb|DV167599.1|DV167599
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|71427481|gb|DR808531.1|DR808531
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|71445134|gb|DR826184.1|DR826184
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|74245787|gb|DT653701.1|DT653701
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|148939985|gb|EC884716.2|EC884716
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|78090189|gb|DV518563.1|DV518563
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|148938546|gb|EC882867.2|EC882867
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|19822147|gb|BQ048171.1|BQ048171
EST:     ACATCATTGTAGCACAGCTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|50338176|gb|CO533302.1|CO533302
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|58029811|gb|CX725238.1|CX725238
EST:     ACATCATTGTAGCACAGCTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|101400189|gb|EB821914.1|EB821914
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|93282145|gb|EB674409.1|EB674409
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|76012850|gb|DT940020.1|DT940020
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|211478510|gb|FL023986.1|FL023986
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|93282646|gb|EB674910.1|EB674910
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|148934818|gb|EC878864.2|EC878864
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|113702266|gb|EE679770.1|EE679770
EST:     ACATCATTGTAGCACAGCTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|101399344|gb|EB821545.1|EB821545
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|71307773|gb|DR790105.1|DR790105
EST:     ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|211478514|gb|FL023990.1|FL023990
EST:     ACATCATGGTAGCACAGCTGCTCTACCTCGACGCTATGGATCCCNATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
EST: gi|26455779|gb|CA827362.1|CA827362
EST:     ACATCATTGTAGCACAGCTGCTCTACCTCGACGCTATTGATCCCAATAAG                         GATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG
genomic: ACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 138

AGAATTATTCGGTGCGGAGGCCCCGTTGAGGATGATATGGCCAACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 174

AGAATTATTCGGTGCGGAGGCCCCGTTGAGGATGATATGGCCAACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

AGAATTATTCGGTGCGGAGGCCCCGTTGAGGATGATATGGCCAACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 63

AGAATTATTCGGTGCGGAGGCCCCGTTGAGGATGATATGGCCAACATCATTGTAGCACAACTGCTCTACCTCGACGCTATTGATCCCAATAAGgtgaaaacga ... cttcctgtagGATATCATTATGTATGTGAATTCGCCAGGAGGGTCAGTGACAGCTG