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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaccgtcatgcttctttcatatctgcgatcaataaattgaatatttgtgtttgtttggttcattgagcctagttcaatcttattgacctttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG

Basic information

species Zea mays
transcript GRMZM2G077278_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 3
-caaccgtcatgcttctttcatatctgcgatcaataaattgaatatttgtgtttgtttggttcattgagcctagttcaatcttattgacctttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG
 |  |||   | |   |||  ||  |    |  ||  |||| |    | || ||   |        |||  || ||   | || ||     ||| |   ||||||||||||||||||||||||||||||| |||||||| | ||| |||||| | ||||||||||| ||||||||||| || |||||||||||||||||||
gcttccgcattacagatttggtaattttt-tatatgcattgtactgatatgcttcagttagcatccgaggataattttcttttgtttgatctttgaattagATCATATCTGGTGTTGAATATTGCCATAGAAACATGGTGGTTCATCGTGATCTTAAGCCAGAGAACCTTCTTTTGGACTCCAAATGCAATGTTAAGATTG

upper sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 3'ss of exon 2
caaccgtcatgcttctttcatatctgcgatcaataaattgaatatt---tgtgtttgtttggttcattgagcctagttcaatctta--ttgacctttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG
     |  |   | |||   | | ||  ||  |    ||||  |||   |||| |  | | | || |   || |   ||     ||  |||  | |  |  ||||||  | ||||| || |||||||||||| |||| ||||||| ||| ||||| || |||||||||||  | ||| | || || ||||| || || ||||| |
----aggtaaattccttggttgtttg-aatggaatttttgaggattctgtgtggtcctcttgctcttcaggcttttatctggtataaattgctcatgctgcgcagATTGTGTCTGGCGTGGAATATTGCCATCGGAATATGGTTGTTCATCGTGACTTGAAGCCAGAGAACTTACTTCTCGACTCCAAATGGAACGTCAAGATAG
















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|91878198|gb|EB408155.1|EB408155
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|149109232|gb|EE190089.2|EE190089
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|71327271|gb|DR800259.1|DR800259
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|74240534|gb|DT648448.1|DT648448
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|149013919|gb|EE043417.2|EE043417
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|211110233|gb|FL282966.1|FL282966
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|211085855|gb|FL313546.1|FL313546
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAA                         ATCATATCTGGTGTTGAATA
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATA
EST: gi|148954916|gb|EC900404.2|EC900404
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|78108756|gb|DV527173.1|DV527173
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|9255242|gb|BE345710.1|BE345710
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|9255371|gb|BE345839.1|BE345839
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGT
EST: gi|76012620|gb|DT939790.1|DT939790
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|9254260|gb|BE344728.1|BE344728
EST:     GCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: GCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|31352455|gb|CD436812.1|CD436812
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGGCACTTTTTTCAGCAG                         ATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGAT
EST: gi|211104121|gb|FL354108.1|FL354108
EST:     TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAG                         ATCATATCTGGTGT
genomic: TTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 304

CTGTGTTGTTATGGAGTATGTTAAATCTGGAGAGTTGTTTGATTACATCGTTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 230

CTGTGTTGTTATGGAGTATGTTAAATCTGGAGAGTTGTTTGATTACATCGTTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 354

CTGTGTTGTTATGGAGTATGTTAAATCTGGAGAGTTGTTTGATTACATCGTTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 313

CTGTGTTGTTATGGAGTATGTTAAATCTGGAGAGTTGTTTGATTACATCGTTGAGAAGGGAAGGCTACACGAAGAGGAAGCCCGACACTTTTTTCAGCAGgtggctttct ... ttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtttgtttggttcattgagcctagttcaatcttattgacctttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG
                                    tattgac  putative branch site (score: 313)
                                          cctttttat  CT-rich tract
                               aatcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaccgtcatgcttctttcatatctgcgatcaataaattgaatatttgtgtttgtttggttcattgagcctagttcaatcttattgacctttttatgcagATCATATCTGGTGTTGAATATTGCCATAGGAACATGGTTGCTCACCGTGATTTAAAGCCAGAGAATCTTCTTTTGGATTCAAAATGCAATGTTAAGATTG

- - - - -tgcttct
- - - - - - - - ttcatat
- - - - - - - - - - - - - - - caataaa