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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttctgggattcctgatgttcaaatgaaaccgaactggttctgaaacagggcctgctctgattgccacgacacgagcaaaattttattacttcttcaatttatggcactgctgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA

Basic information

species Zea mays
transcript GRMZM2G031308_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031308_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g53520.2 (Oryza sativa), 3'ss of exon 2
gtgagcttctgggat-tcctgatgttcaaatgaaaccgaactggttctgaaacagggcctgctctgattgccacgacacgagcaaaattttattacttcttcaatttatggcactgctgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA
|||||||||||   |    |||   | |   |     || | |   |||  |   |   ||| ||| ||| || |         |   | |||     |   || ||||   |||| |  |||| |||||||| || |||||||||||||| ||||| || |||||  || | || ||  ||||||| || ||||||||||||||||| || || ||||| ||||| 
gtgagcttctgtagtactttgactctgatgcgctttagacccgcagctggtatttgtggtgccctg-ttgtcaagtttttccttatcatgtat-gtggccataacttattatactgat--tttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAACATTGCCCTTTCTCTGAGATATGAGATCAATAGAGGTTTTGCAACCTTG
















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|32806427|gb|CD958661.1|CD958661
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
EST: gi|211304744|gb|FL369602.1|FL369602
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCCGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|60354473|gb|DN221446.1|DN221446
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|32826408|gb|CD966086.1|CD966086
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACGA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
EST: gi|60343056|gb|DN210029.1|DN210029
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|60672364|gb|DN475124.1|DN475124
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCCGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|60672324|gb|DN475087.1|DN475087
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCCGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|78543726|gb|DV621224.1|DV621224
EST:     CGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: CGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|32791931|gb|CD944167.1|CD944167
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAACGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
EST: gi|60398300|gb|DN231116.1|DN231116
EST:     GTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: GTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|32846671|gb|CD986352.1|CD986352
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|32807786|gb|CD960020.1|CD960020
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCGGTTA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
EST: gi|32826664|gb|CD966342.1|CD966342
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGC
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGC
EST: gi|211481757|gb|FL381851.1|FL381851
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATTAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|78080520|gb|DV508932.1|DV508932
EST:     AATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: AATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|32806523|gb|CD958757.1|CD958757
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
EST: gi|32809028|gb|CD961262.1|CD961262
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCCGTTA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTA
EST: gi|148958760|gb|EC905039.2|EC905039
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|111991211|gb|EE332402.1|EE332402
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCCGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|22473080|gb|BU037560.1|BU037560
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|149070242|gb|EE158642.2|EE158642
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|213168588|gb|FM186721.1|FM186721
EST:     TCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|32805872|gb|CD958106.1|CD958106
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCAAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCT
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCT
EST: gi|38502736|gb|CF972596.1|CF972596
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCCGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
EST: gi|60397050|gb|DN229869.1|DN229869
EST:     TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAA                         GTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA
genomic: TCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAA

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), 47 (downstream exon)
Score: 588

AGGTCATGGAGTACCATCTCCTCACCTTGGTGTGCCACTGTCTCATCCTCTCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 529

AGGTCATGGAGTACCATCTCCTCACCTTGGTGTGCCACTGTCTCATCCTCTCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 580

AGGTCATGGAGTACCATCTCCTCACCTTGGTGTGCCACTGTCTCATCCTCTCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 712

AGGTCATGGAGTACCATCTCCTCACCTTGGTGTGCCACTGTCTCATCCTCTCGCTGGCCATCCTCTTCCTGTGGTCCAATGCCTCCACTTTCATCAACAAgtgagcttct ... tgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgacacgagcaaaattttattacttcttcaatttatggcactgctgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA
                                          tgctgat  putative branch site (score: 712)
                                                ttttc  CT-rich tract
           aaaattttattacttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttctgggattcctgatgttcaaatgaaaccgaactggttctgaaacagggcctgctctgattgccacgacacgagcaaaattttattacttcttcaatttatggcactgctgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA