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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttttatggctctcggttttgctgtactgatgcatctggtcaataacttctatgctttattttaaattcacaacttctaaaaaaaactctcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG

Basic information

species Zea mays
transcript GRMZM2G144372_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 4
agttttatggctctcggttttgctgtactgatgcatctggtcaataacttctatgctttattttaaattcacaacttctaaaaaaaac-----tctcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG
   |  | | |||    ||||   | | |||   |||  |   |  ||| |   |     | || |||| |||||  || |    ||      | |   |  ||||| |||| ||||||||| |||||||||||||||||||||||||| |||||||||||||||| ||| ||
--atccacgtctcc---ttttttagcattgagttatcacgcacaacactacagcgtgacctgttgaatttacaacagctgagctgaatgtgttttttaccttcagGTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG
















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|71428528|gb|DR809578.1|DR809578
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|67038589|gb|CO464901.1|CO464901
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|89758156|gb|DY687449.1|DY687449
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|148982506|gb|EE028351.2|EE028351
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|61117886|gb|DN558847.1|DN558847
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|76012958|gb|DT940128.1|DT940128
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|67023340|gb|CO452089.1|CO452089
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|9824919|gb|BE575016.1|BE575016
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|211396452|gb|FL097333.1|FL097333
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|116818640|gb|EC861688.1|EC861688
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAT                         GTGCGAGCAGCGGAATATACTAATGTAACGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|33104344|gb|CF064304.1|CF064304
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|21987710|gb|BQ779238.1|BQ779238
EST:     TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
EST: gi|67022208|gb|CO450957.1|CO450957
EST:     -TGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG                         GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC
genomic: TTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAAC

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: 234

GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 281

GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 327

GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAGgtttgattgc ... tcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttctatgctttattttaaattcacaacttctaaaaaaaactctcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG
                              ttctaaa  putative branch site (score: 327)
                                          ctctcttcccc  putative PPT
           tttattttaaattcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttttatggctctcggttttgctgtactgatgcatctggtcaataacttctatgctttattttaaattcacaacttctaaaaaaaactctcttccccagGTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - tttgctg
- - - - - - - - - - - - - -ctgatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa