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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG

Basic information

species Zea mays
transcript GRMZM2G128171_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG
                                                                                  ||| | | |     |||  |  |||    |||  | | |  ||  |         |  ||  | ||  |||     |  ||| |   |    ||   |||| ||  |     || |||||||||  ||| | |||||| |||||||| |||||||||||||||||||||||||||||||| |||||||  ||||| |||| |||||||||||||
----------------------------------------------------------------------------------atgttatgggcatgcttccagcactttaaactcatgtcttgttcta--------tattttgat-ttcatgatgcactacataagttttgacttgc-tttatgacttt----tagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG

upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G01750.3 (Glycine max), 3'ss of exon 7
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctata--cgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG
                                                                                             |  |  ||  ||  |   || |  | |     | |    ||||      | |||| |  || || |  |||   | | | | ||| |   || | | |    ||||||||  || ||||||||||||||||||||||| ||||||||||| ||||||||||||||||| || |  || |  || ||||||| |||||||||    
---------------------------------------------------------------------------------------------ttacggtggttaagaaa-acaaaaaatccagcgaagaggataaagatggaatattac-aacatgataaataattgaagtttgctgga---ataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 8
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG
                                                                                   |  || |  ||  |||    | | ||||| || | |     || || | |  |  | |||  |  |   |  |  |      | | | | ||| |   || | | |    |||||| |  || ||||||||||||||||||||||| ||||||||||| ||||||||||||||||| || |  || |  || ||||||| |||||||||    
-----------------------------------------------------------------------------------tattcatagttgtcttcct-ttcaagtca-taatgtga---tggaatatacgaatcgttacaacatgataaataatt-----gaagtttgctgga---ataatatttatgcagGTACGACGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGACTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG
                                                                                         ||  | |  |   ||  |  |   ||   | | |||  |  |  |   |  | || ||||  ||  ||   | | |  ||| ||    | ||  ||    | | ||| ||||| |||||||| | ||||||  ||||||||||||||||| | ||||||||||||||||||||| |||| |   | || |||| ||| |||||    
----------------------------------------------------------------------------------------gtgagtacagtgacattttgatt--tatcttctatttaaactaggtgg-atatcat-atttaagaaatgca-tgtgcctaatttagaaaattttcca----ata-cagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA

upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG
                                                                    |  || || |  ||||  | |  |||  |||  | |  ||   |||||     ||| | | ||             |||||  ||  ||   | | |  ||| ||    | ||  ||    | | ||| ||||| |||||||| | ||||||  ||||||||||||||||| | ||||||||||||||| ||||||| || |   | || |||| ||| |||||    
--------------------------------------------------------------------gtgagtacagtggcatattttgatttatcttctagt--taa--actag-----gttggtatca-------------tatttaagaaatgca-tgtgcctaatttagaaaatttgcca----ata-cagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA

upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG
                                                                                             |  |  ||  ||  |   || |  | |     | |    ||||      | |||| |  || || |  |||    |  |  ||     || | | |    ||||||||  || ||||||||||||||||||||||| ||||||||||| ||||||||||||||||| || |  || |  || ||||||| |||||||||    
---------------------------------------------------------------------------------------------ttacggtggttaagaaa-acaaaaaatccagcgaagaggataaagatggaatattac-aacatgataaataattgaagt-ttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacg--caatatactgtacttatcacactacat-cagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG
                                                                                                    | |   | |  ||  | ||||  ||   ||  ||   ||  | | |  ||     ||||  |||    ||| | |        |  ||  || || ||| |||||||| |||||||| || || ||||| || ||||||||||  |||||||||||| | |||||||| || |  ||||| || | ||||||||| |  
----------------------------------------------------------------------------------------------------gtaagttgg--acaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC

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|149086778|gb|EE176319.2|EE176319
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
EST: gi|148936842|gb|EC880983.2|EC880983
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
EST: gi|148972619|gb|EE023578.2|EE023578
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAACCAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
EST: gi|71324810|gb|DR799111.1|DR799111
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
EST: gi|31358980|gb|CD443337.1|CD443337
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
EST: gi|78117470|gb|DV535857.1|DV535857
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGG-AAACAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
EST: gi|78118070|gb|DV536457.1|DV536457
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
EST: gi|148932445|gb|EC876161.2|EC876161
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTTTGA-GTTTTTCC-AA-GGGAAAC
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTT--GAAGTTTTTCCCAAAGGGAAAC
EST: gi|67015622|gb|CO444371.1|CO444371
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAA
EST: gi|149081234|gb|EE170345.2|EE170345
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAAAGTTTT-CCCAAAGGGAAACA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAA-GTTTTTCCCAAAGGGAAACA
EST: gi|148959024|gb|EE010535.2|EE010535
EST:     GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAA                         GTATGGAGTTAGTGGATTTCCTACCTTGAA
genomic: GTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAA

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), 48 (downstream exon)
Score: 167

ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 409

ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 502

ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 532

ACGTATGAGAAGGTGGCTTCTGTTTTCAAGTTGGATGAAGGAGTTGTTATTGCTAACCTTGACGCTGACAAACACAGGGATTTGGCTGAGAAgtatgttctg ... actacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG
      ttctgac  putative branch site (score: 532)
                          aatatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA