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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattcagaataaaaatgttccaatgtgatcaccgtgtggacttgttcataatttggaaatactgcaaaacctctgcag

Basic information

species Zea mays
transcript GRMZM2G370852_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g03260.3 (Oryza sativa), 5'ss of exon 11
GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgata--ttcag-----aataaaaatgttccaatgtgatcaccgtgtggacttgttcataatttggaaatactgcaaaacctctgcag
|| |||||||||||||||||||| || || || || || |||||||||||||||  | |||     |  ||| |  | |  |  |||||| | |||||  | | |  ||||     || | ||  ||| || || ||
GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatgcagcaaacagcaaacacatactgaaatgatcatcctgtggtttcgatt-taat--aataagaatgttaaatctatgtag

upper sequence: GRMZM2G370852_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 13
GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattcagaataaaaatgttccaatgtgatcaccgtgtggacttgttcataa---tttggaaatactgcaaaacctctgcag--------------------------------------------
||||||||||| |||||||||||||||||||||||||| || ||||||||        | ||||   |||| || ||| |     |  | || |||||   ||   | | |||||    ||      ||  |                                             
GGAAAGAAGGTCAAAGTTCCCACATTCCTTGTCCCTGCAACCCAAAAGgt------ttgtataatt-tgttgcactgtaagtgttg-atagatttgttgggaagattctagaaatttatcatgggaactagattaatcataaatggattatagtaattcatatattaaaatcttcag

upper sequence: GRMZM2G370852_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 13
GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtg------atattcagaataaaaatgttccaatgtga---tcaccgtgtggacttgttcataatttggaaatactgcaaaacctctgcag-----------------------------
||||||||||| |||||||||||||| ||||||||||| || ||||||||        ||||     |  |    ||   |||  |   ||    |  ||| |||| ||||    ||||| | |  ||  |||  |||                              
GGAAAGAAGGTCAAAGTTCCCACATTTCTTGTCCCTGCAACCCAAAAGgtttgtactgtatttttgcttgatggatttgtatggaagattccaaatagggatttgt-cata----ggaaagagtttaat-cctacgcaatatagtaattgatatgataaaattatcag

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|149051576|gb|EE155676.2|EE155676
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGAGGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|37375881|gb|CF624420.1|CF624420
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|32787622|gb|CD936524.1|CD936524
EST:     TAAAGTTCCCACATTCCTTGTACCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATC
genomic: TAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATC
EST: gi|76282892|gb|DV022460.1|DV022460
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|24765664|gb|CA400823.1|CA400823
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTACCACACAAAAG                         GTGTGGATGGACGTATATACCCTTCCTGTAACAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|71771493|gb|DR969430.1|DR969430
EST:     AAAGAAGGTTAAAGTTTCCACATTTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: AAAGAAGGTTAAAGTTCCCACA-TTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|76924561|gb|DV170009.1|DV170009
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|101395254|gb|EB819557.1|EB819557
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|16916456|gb|BM072849.1|BM072849
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|31350830|gb|CD435187.1|CD435187
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|60341015|gb|DN207988.1|DN207988
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|78076215|gb|DV504649.1|DV504649
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|32840107|gb|CD979788.1|CD979788
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTA
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTA
EST: gi|211090106|gb|FL396339.1|FL396339
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|71445105|gb|DR826155.1|DR826155
EST:     ATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: ATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|71763036|gb|DR960973.1|DR960973
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|32840106|gb|CD979787.1|CD979787
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTA
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTA
EST: gi|211011802|gb|FL408548.1|FL408548
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|149080159|gb|EE169177.2|EE169177
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCTTTGTCCCTGCCACACAAAAG                         GTGTGGAGGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|211350370|gb|FL368852.1|FL368852
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|148971978|gb|EE022780.2|EE022780
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|74246484|gb|DT654398.1|DT654398
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|149079940|gb|EE168953.2|EE168953
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|37418663|gb|CF647003.1|CF647003
EST:     GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT
EST: gi|110195844|gb|EC877741.1|EC877741
EST:     CCCACATTCCTTGTCCCTCCCACCCAAAAG                         GTGTGGATGGACGTATATAGCCTTCCTTTACCAGGATCTGGCGGCAAAACT
genomic: CCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACT

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: 47 (upstream exon), 33 (downstream exon)
Score: 25

GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACTTGCGCCCAGATATTCGAGGAGGCTGGTTGTGATACACCAGCAAGTCCTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 7

GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACTTGCGCCCAGATATTCGAGGAGGCTGGTTGTGATACACCAGCAAGTCCTA


Block sizes: 45 (upstream exon), 25 (downstream exon)
Score: 8

GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACTTGCGCCCAGATATTCGAGGAGGCTGGTTGTGATACACCAGCAAGTCCTA


Block sizes: 40 (upstream exon), 44 (downstream exon)
Score: 10

GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattca ... acctctgcagGTGTGGATGGACGTATATAGCCTTCCTGTACCAGGATCTGGCGGCAAAACTTGCGCCCAGATATTCGAGGAGGCTGGTTGTGATACACCAGCAAGTCCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgatattcagaataaaaatgttccaatgtgatcaccgtgtggacttgttcataatttggaaatactgcaaaacctctgcag

- AAAGAA
-  AAGAAG