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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcag

Basic information

species Zea mays
transcript GRMZM2G006130_T08
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T05 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 5'ss of exon 15
TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcag
|||| | ||||||||||||||||| || ||||||||||||||| ||||||| ||||||||||| ||  ||  |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||
TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAACgttagttttgatgactccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcag

upper sequence: GRMZM2G006130_T05 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 14
-------------------------------------------TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcag
                                           |||| | ||||||||||||||||| || ||||| ||||||||| ||||||| ||||||||||| ||  ||| |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||
TGCAATGAGATATTTACTGTAACTTCTTGTTGGTTCTTTGCAGTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAACgttagttttgatggctccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcag

upper sequence: GRMZM2G006130_T05 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os12g03470.2 (Oryza sativa), 5'ss of exon 15
TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgc-tgcgatgattttgtttcgaacaaaacgagatcag
|||| | ||||||||||||||||| || ||||| ||||||||| ||||||| ||||||||||| ||  ||| |   |     || || ||||  ||||   |||  | ||||   | |  | ||  || ||| | ||||     |||||
TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAACgttagttttgatggctccatggtttctttatttgtgttttt---gtttatttaacaagtactgtaataatgcttcaatcaaac---aatcag

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|211495379|gb|FL350690.1|FL350690
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211098336|gb|FL317177.1|FL317177
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211378660|gb|FL357038.1|FL357038
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211258110|gb|FL346334.1|FL346334
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|18654846|gb|BM499651.1|BM499651
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
EST: gi|211474807|gb|FL320108.1|FL320108
EST:     GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC                         GTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC
genomic: GTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCC

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), 49 (downstream exon)
Score: 179

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 764

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 492

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 343

TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattc ... acgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAACgttagtattcttggttttttttaccctctacttgttcttttcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcag

- - - - - CAGATG