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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaatagcaatctgcatatagtccatatccatcactatttgcacccactggtttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG

Basic information

species Zea mays
transcript GRMZM2G152888_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
-----------------ctaatagcaatctgcata--tagtccatatccatcactatttgcacccactggt--ttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG
                  |  ||   |||| || |  | || || |   ||   | ||  ||     | ||  |||  |   ||    |  | ||  ||| ||  |  |||    || |||||||||||||| ||||| || || ||||| |||||||| || ||||| ||||| ||||| |||||||||||||| || ||||||||||||||||| ||||
gttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG

upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 10
ctaatagcaatctgcatatagtccatatccatcactatttgcacccactggtttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG
 | | | ||      ||  |           ||  | ||   ||||       |          || ||| |    |  | ||  ||  || | || |||||||||||||| || || || |||||||| || || || || || ||||| |||||||||||||| |||||  | ||| | ||||| ||||| || ||||
gtgagaacatcaaatatccaactatctatgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaat-tttttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG

upper sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------------------------ctaata-gcaatctgcatatagtccatatccat--cactatttgc-acccactggtttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG
                                                                    ||||   |   | ||  |  | ||| |  ||  ||||  |    |  | |  |||    |   | | | || | | ||| | | ||| || |  | ||||||||||||||||| || ||||| ||||| || || || |||||| | || |||||||| || |||||||||||||| ||||| ||||| |||||||| ||||
gtaagctttatctttaatttctatacattcaccattcatgtcttttcattcttgattaaagtagctgcaatacagagattccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggc-tagtattgacaagtta-tgctgttccagGTTGCTGTTGTGACAGTTGCTTTTCCAGCTACTCCACTTCTTTTGGCCAGGGCACGGATCTGCATTTCTGCTTCTCATACCAGGGAAGACCTGATTAAAG

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|211256092|gb|FL474863.1|FL474863
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|32834771|gb|CD974449.1|CD974449
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|22545658|gb|BU098017.1|BU098017
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAG-GCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|213170493|gb|FM189407.1|FM189407
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|32846670|gb|CD986351.1|CD986351
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|71306654|gb|DR789487.1|DR789487
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|78083289|gb|DV511682.1|DV511682
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|87157213|gb|DY402002.1|DY402002
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|78078704|gb|DV507116.1|DV507116
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|60341232|gb|DN208205.1|DN208205
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|32835583|gb|CD975261.1|CD975261
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|76011503|gb|DT938673.1|DT938673
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGTTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|161594466|gb|EY963847.1|EY963847
EST:     CGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTCCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: CGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
EST: gi|86471728|gb|DY238098.1|DY238098
EST:     ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAG                         GTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG
genomic: ACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGG

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), 49 (downstream exon)
Score: 92

TTTTGAGGTTCTTGGTGACAATGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

TTTTGAGGTTCTTGGTGACAATGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 132

TTTTGAGGTTCTTGGTGACAATGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 106

TTTTGAGGTTCTTGGTGACAATGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCTAAGATTCCTGCATTCTCTAGGGAGTGCCTTAGACAAAAGgttagtagta ... tatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactggtttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG
                                           cttatcttcc  CT-rich tract
                                 ttataagatacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaatagcaatctgcatatagtccatatccatcactatttgcacccactggtttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - -ctgcata
- - - - - - - - - - - - - - ccatcac
- - - - - - - - - - - - - - - - - - - ttgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtact