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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttggtgctgagatcagtacttattttggatacctaattgggatactttgccgcacgtacccacaggatttctgatagtattctttgcacatttgatccatctttctttgcaagcacaacagcacatgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG

Basic information

species Zea mays
transcript GRMZM2G362088_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 4
gta---atttggtgctgagatcagtacttattttggatacctaat--tgggatact-ttgccgcac-gtacccacaggatttctgatagtattct--ttgcacatttgatccatctttct--ttg--caagcaca---acagcacatgcatgtt-tttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG
|||   ||   |  ||  | |     ||| ||           ||  ||| || || |||  |||    |  ||  || ||| ||| |   ||||  | | |  | | |   || |||    |||  | | |  |    |  ||||||||| |  |||  || ||||||||         ||||  | |  | |||||| ||||||||||||||||| || ||||||||||||||||||||||||||| |||||||||| || ||||| ||||| |||||||||||||||||||| || |||
gtacacatacagcactatggttttagcttcttccaatcttgggataatggcatgctgttggtgcattagaagcattggttttgtgagaaagttctagtagtatgtgttactgatttttacaattgatccatcttacgtgccacacatgcatatggtttttctcaatcaagaactc-----attggta-ccagccaattttagGTATGCTGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 4
gtaatttggtgctgagatcagtacttattttggatacctaattgggatactttgccgcacgtacccacaggatttctgatagtattctttgcacatttgatccatctttctttgcaagcacaacagcacatgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG
                                             |  ||| |     |  |  |||   ||||  | |||  ||   ||| |||    | ||||  || |||       |||||  | |||    ||||||    ||  || | |  |     |||  |  || || |||||||||| ||||| || || ||||| || ||| | || || || | |||| || |||| |||||||||||||| || ||||| || |||||||||||||| |||
---------------------------------------------gtgactctcatttatctttcca---gattaatcata--atctattgtaca----aaccattctttttt-------caacaaaaaatg---atttttg----aaataaaatttgt-----ttgctaa-ttctctatttcagGTACGCTGCGTTAGCACCACTCTATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 4
gtaatttggtgctgagatcagtacttattttggatacctaattgggatactttgccgcacgtacccacaggatttctgatagtattctttgcacatttgatccatctttctttgcaagcacaacagcacatgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG
                                                        |    |  | |      ||   | | ||| | |  |  |||  |   | | |||||    |   ||||| || |||    |||||   ||||   | | |  |     |||  |  || ||  ||||||||||||||| || || || || || ||| | || || || | |||| || |||| |||||||||||||| || ||||| || |||||||||||||| |||
--------------------------------------------------------gtgactgtc-atttatctttccagattatgcataacctattgtacaaaccattctt----atttcaacaacaaatg----ttttt---tgaaatgaaatttgt-----ttgctaa-ttatctgtttcagGTATGCTGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 4
gtaatttggtgctgagatcagtacttattttggatacctaattgggatactttgccgcacgtacccacaggatttctgatagtattctttgcacatttgatccatctttctttgcaagcacaacagcacatgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG
|||  |   ||   |   || |  || |  ||   |||||  ||    ||||| |   |   |     |  |  ||   |  || ||||      | |  |  |       | |    | |       |||| |          |||   || | |   ||| ||    |  |  |     |||||||||||||  |||| |||||||||||  |||| ||||| | |||| |||| || |||||||||||||| || |||||||| | ||||||||||||||||
gta--tcattggccaacccattttttttcctgttcacctatctg----acttt-ctaaattcaatagaaataactcaacttatagtcttcttgagtctattgaaatggatctagagctctctctcttccatgaaaaccc--atttgag--aaaattacagaggat---aacttcatt--cctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGTAGTGTATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGG

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|211329193|gb|FL235162.1|FL235162
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211329196|gb|FL235165.1|FL235165
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211331350|gb|FL235175.1|FL235175
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAA
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAA
EST: gi|211329203|gb|FL235172.1|FL235172
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211331353|gb|FL235178.1|FL235178
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|50330001|gb|CO525127.1|CO525127
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211329194|gb|FL235163.1|FL235163
EST:     GATTCAACAATAGTGAAGTTTGANATTTGGGATACTGCTGGGCAAGAKAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGC
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGC
EST: gi|148937431|gb|EC881612.2|EC881612
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211331363|gb|FL235188.1|FL235188
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATT
EST: gi|5525847|gb|AI861740.1|AI861740
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCATTTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211331355|gb|FL235180.1|FL235180
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCA
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCA
EST: gi|60336834|gb|DN203807.1|DN203807
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211331359|gb|FL235184.1|FL235184
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTTACTACAGAGGAGCTGCTGCTGCAATTG
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTT-ACTACAGAGGAGCTGCTGCTGCAATTG
EST: gi|211331360|gb|FL235185.1|FL235185
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211329201|gb|FL235170.1|FL235170
EST:     GATTCAACAATAGTGAAGTYTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211331364|gb|FL235189.1|FL235189
EST:     GATTCAACAATAGTGAAGTTTGADATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTG
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTG
EST: gi|78089132|gb|DV517518.1|DV517518
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211329204|gb|FL235173.1|FL235173
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211331358|gb|FL235183.1|FL235183
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGGCGCCACTTTACTACA
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGG-CGCCACTTTACTACA
EST: gi|211329197|gb|FL235166.1|FL235166
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
EST: gi|211329200|gb|FL235169.1|FL235169
EST:     GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG                         GTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT
genomic: GATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGT

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: 258

GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 440

GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 507

GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggt ... tcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG
                                             tcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttggtgctgagatcagtacttattttggatacctaattgggatactttgccgcacgtacccacaggatttctgatagtattctttgcacatttgatccatctttctttgcaagcacaacagcacatgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcagGTATGCTGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG