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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacttttttaactaaataaactgtctgtaggttatttgttatacttctatcctttccgttttatagagagagacacatacattgtcgtgtagtagtgcctaacaaatgacttctgtgatggtaactccaatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACAATGGATATTAGTGGAGAACAGCACCAGGACATT

Basic information

species Zea mays
transcript GRMZM2G044457_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044457_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 2
gttagtacttttttaactaaataaactgtctgtaggttatttgttatacttctatcctttccgttttatagag-agagacacatacat----------tgtcgtgtagtagtgccta---acaaatgacttctgt--------gatggtaactccaatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACAATGGATATTAGTGGAGAACAGCACCAGGACATT
||||||| || ||| | |   ||||||   |  | || || |||| |||||||||  ||||   | || |  | | |  |   |  ||          |    | |  | |   |||      |||   | ||||         ||| |||  |   ||| ||||||||  | ||||||| |||  |||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| || ||||||
gttagtatttatttgattgt-taaactagattcatgtcatatgttgtacttctattgtttctagtataaaatgcatactcttttgtatgctattcacttacaatctgttgggaactaggtgtgaatatttcctgttaacttctaatgctaaaactgttttgcagTTTGACGTAACTTTTCCGAGTGTTCCCTGCACCCTTCTCAGTGTTGATACCATGGATATTAGTGGAGAGCAGCATCATGACATT
















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|88756247|gb|DY540388.1|DY540388
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|211345912|gb|FL043763.1|FL043763
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|28910351|gb|CB331395.1|CB331395
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGC
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGC
EST: gi|32829302|gb|CD968980.1|CD968980
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|211345911|gb|FL043762.1|FL043762
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|211345907|gb|FL043758.1|FL043758
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTCGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|149111503|gb|EE295005.2|EE295005
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|211345905|gb|FL043756.1|FL043756
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|211345906|gb|FL043757.1|FL043757
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|91873243|gb|EB403200.1|EB403200
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|211345910|gb|FL043761.1|FL043761
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|211345908|gb|FL043759.1|FL043759
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTCGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|148944284|gb|EC889380.2|EC889380
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|50334991|gb|CO530117.1|CO530117
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|149090670|gb|EE179995.2|EE179995
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|67035454|gb|CO463987.1|CO463987
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
EST: gi|149027104|gb|EE046395.2|EE046395
EST:     AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAAT                         TTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA
genomic: AGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACA

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: 46 (upstream exon), 49 (downstream exon)
Score: 121

GGTCATATTTTTATTCAGCAACAGAGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACAATGGATATTAGTGGAGAACAGCACCAGGACATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

GGTCATATTTTTATTCAGCAACAGAGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACAATGGATATTAGTGGAGAACAGCACCAGGACATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

GGTCATATTTTTATTCAGCAACAGAGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACAATGGATATTAGTGGAGAACAGCACCAGGACATT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 206

GGTCATATTTTTATTCAGCAACAGAGACTAAGTTAGTTGTGGACACATCAAGAGGAGAAAGGCTACGAGTAAATgttagtactt ... caatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACAATGGATATTAGTGGAGAACAGCACCAGGACATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcgtgtagtagtgcctaacaaatgacttctgtgatggtaactccaatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACAATGGATATTAGTGGAGAACAGCACCAGGACATT
                                    tggtaac  putative branch site (score: 206)
                 taacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtacttttttaactaaataaactgtctgtaggttatttgttatacttctatcctttccgttttatagagagagacacatacattgtcgtgtagtagtgcctaacaaatgacttctgtgatggtaactccaatttacagTTTGATATTACTTTTCTGAGCATTCCTTGCACCCTCCTCAGCGTTGATACAATGGATATTAGTGGAGAACAGCACCAGGACATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA