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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctacagtattggggactacctcattccttaatcatctgatatctgtttcatccttttgttcttggagttatatcatatttcatgcttatatttgtgtgatttttacaacaatgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC

Basic information

species Zea mays
transcript GRMZM2G590033_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g13730.1 (Oryza sativa), 3'ss of exon 4
------------------------------------gtactgctacagtattggggactacctcattcc------ttaatcatctg---atatctgt-ttcatcct-tttgttcttggagttat--atcatatttcatgcttatatttgtgtgatttttacaac-aatgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC
                                     |  | ||    ||||  | || | ||| |  |      ||  ||||||    |||||  | | |||  |  | | |   | |||| |  || || |  | | | |||     | |  ||||    || ||  | |||||||||||||| || |||||||| || || ||||||||||| || |||||  | ||||| || |||||||||||||| ||||||||||| |||||||||||
gtactaatataacagtggtgatactctcgccagaggatcatccttttttattatgtacaaactcgtggcaccagtttgttcatctatgcatatccttgtccatattgctagctagagcagttcttaattatgtcacttacatatgccattttctttttgttgactaacaaaaacagGAAGACAGTCTGCCAGTTCCCTGGACATCAGGGTGCTGTGAGGGGTTTGGCGACATCTACTGATGGTGATCTTCTAGTATCATGTGGTGTTGACTGCAC

upper sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0028g03140.t01 (Vitis vinifera), 3'ss of exon 4
gtactgctacagtattggggactacctcattccttaatcatctgatatctgtttcatcct-tttgttcttggagttatatcatatttcatgcttatatttgtgtgatttttacaacaatgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC
                    | ||  | |||    |||  |||  | ||| | ||   || | | |   |  |  |||||  |  ||     |||  |||   | ||||| | ||       |  |||   |||||||||||||| || || ||||| ||||||||| | ||||| ||| |||||||||||||     ||||||||||||||||   ||| |||||
------------------ataatatgtaattga--aattctcttctctctctctctctctatctatctatctatatatatatttcttttcttttaatttttctttattttcataa-------actagGCGAACAGTTTGTCAGTTTCCTGGTCACCAAGGTGCTGTACGGGGTTTGACAGCATCCACAGATGGACGCATTCTTGTATCATGTGGAACTGATTGCAC
















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|32868106|gb|CF007788.1|CF007788
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|67042521|gb|CO468776.1|CO468776
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|76020037|gb|DT947207.1|DT947207
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|50322924|gb|CO518050.1|CO518050
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|50322960|gb|CO518086.1|CO518086
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211134814|gb|FL053070.1|FL053070
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGC
EST: gi|211134816|gb|FL053072.1|FL053072
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTC
EST: gi|50323384|gb|CO518510.1|CO518510
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211135752|gb|FL053081.1|FL053081
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGG
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGG
EST: gi|211135757|gb|FL053086.1|FL053086
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTT
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTT
EST: gi|50323230|gb|CO518356.1|CO518356
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTCTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|50322944|gb|CO518070.1|CO518070
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCC
EST: gi|149009868|gb|EE041735.2|EE041735
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|9732526|gb|BE511278.1|BE511278
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|50323367|gb|CO518493.1|CO518493
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211136700|gb|FL053097.1|FL053097
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211136696|gb|FL053093.1|FL053093
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAG
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagG-AAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAG
EST: gi|211134819|gb|FL053075.1|FL053075
EST:     ATGT-CGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGG
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGG
EST: gi|78025063|gb|DV493450.1|DV493450
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211134817|gb|FL053073.1|FL053073
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211135748|gb|FL053077.1|FL053077
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAG
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAG
EST: gi|71449370|gb|DR830420.1|DR830420
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211134818|gb|FL053074.1|FL053074
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGT
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGT
EST: gi|9733356|gb|BE512213.1|BE512213
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211134815|gb|FL053071.1|FL053071
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCSCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211135751|gb|FL053080.1|FL053080
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|50323075|gb|CO518201.1|CO518201
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|89252964|gb|DY624750.1|DY624750
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|78085348|gb|DV513741.1|DV513741
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|93281014|gb|EB673278.1|EB673278
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|50339131|gb|CO534257.1|CO534257
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211136701|gb|FL053098.1|FL053098
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GTAAGACAGTTTGTTCAGTTCCCCGGGCACCAGGGTGCT
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagG-AAGACAGTTTGT-CAGTTCCCCGGGCACCAGGGTGCT
EST: gi|211135760|gb|FL053089.1|FL053089
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTT-AAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211136695|gb|FL053092.1|FL053092
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGG
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGG
EST: gi|71772085|gb|DR970022.1|DR970022
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
EST: gi|211135758|gb|FL053087.1|FL053087
EST:     ATGTTCGCCTTTGGGATATTGCTGCGAG                         GAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC
genomic: ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAAC

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: 28 (upstream exon), 49 (downstream exon)
Score: 123

ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC


Block sizes: 28 (upstream exon), 49 (downstream exon)
Score: 165

ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC


Block sizes: 28 (upstream exon), 49 (downstream exon)
Score: 136

ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC


Block sizes: 28 (upstream exon), 49 (downstream exon)
Score: 84

ATGTTCGCCTTTGGGATATTGCTGCGAGgtactgctac ... atgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatatcatatttcatgcttatatttgtgtgatttttacaacaatgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC
                                 atttttacaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgctacagtattggggactacctcattccttaatcatctgatatctgtttcatccttttgttcttggagttatatcatatttcatgcttatatttgtgtgatttttacaacaatgacaacagGAAGACAGTTTGTCAGTTCCCCGGGCACCAGGGTGCTGTAAGAGGTTTAACAACATCCACAGATGGTGATCTTCTTGTATCATGTGGCGTTGACTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG