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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttacaagctgtgttatgtttgttccttcccttaggatctacctgtaaccatgacttcttattcttgttaatcggtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC

Basic information

species Zea mays
transcript GRMZM2G370852_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
gtaagcttacaagctgtgttatgtttgttccttcccttaggat-ctacctgtaacca-tgacttcttattcttgttaatcggtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC
|||||  |||||  |   || | | | || ||   ||||   | ||||| | |     | |   || || ||   |||| | || || |||||||||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||  
gtaagactacaaaatac-ttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 8
---------------------------------------gtaagcttacaagctgtgttatgtttgttccttcccttaggatctacctgta-accatgacttcttattcttgttaatcggta------cttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC
                                         | |||   || |   |||||||    |   |   |||  |      |||      |   ||| |  | |||  | | |  |      | | ||||| |||||||| || || || ||||||||||| || ||| ||||||||||||||||  ||||  | |||||| |||  
gtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgacatgagtatattataacactgttgtctgttttcttttcgtggtgttgccatttgaaaaaccatcattcagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 7
------------------------------------------gtaagcttacaagctgtgttatgtttgttccttccctt--aggatctacctgtaaccatgacttcttattcttgttaatcggta---cttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC
                                          | |     |  || ||   |||| |||||   ||  ||  | |    |  | |||  || || || |    |   |    |||    |||||||||||||||||| ||  | ||  |||||||||| || ||||||||||||||||| ||  ||||||| |||||| |||| 
agtaagtgccttgattctgtacttttgtttctgttggacatagcatagccatcaggtg-actatgattgtttgctcattttcatgcagcaaatataaaaattacatccttacatgaatggatggtttaccttacaGATTATTGGTGAAATAACTGTGGCTGGTGCAACATATAAATCGATGGAGTTTGTCGGTACAACTGTTGAAAGTTTAAC-

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 7
-------------------------------------------gtaagc-ttacaag-ctgtgttatgtttgttccttcccttaggatctacctgtaaccatgacttcttattcttgttaatcggta---cttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC
                                            || || |||   | | ||| | || ||| || ||  | |       |  | |||  || || || |    |   | |  |||    |||||||||||||||||| ||  | ||  |||| ||||| || ||||||||||||||||||||  |||| || |||||| |||| 
gtaagttccttgattctgaacttttgtttctgttggacatatcataggcattaggtgaccgtgat-tgcttgctcattttcatgcagcaaa--tataaaaattacatccttacatgaatgaatggtttaccttacagATTATTGGTGAAATAACTGTGGCTGGGGCAACATATAAATCGATGGAGTTTGTTGGTACAACCGTTGAAAGTTTAACT

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 7
---gtaagcttacaagc-tgtgttatgtttgttccttcccttaggatctacctgtaaccat-gacttcttatt--cttgttaatcggta------cttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC
   ||  |  |    |  |||||||   ||     ||   |   | | ||| |  |   || ||  | |||||   | || ||  |||       ||| |||||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||||||||    ||||| |||||||| || 
tatgtgtgtgtgtgtgtgtgtgttaaacttaa--atttgttggtgttttacttaaatttattgatgttttattggttggtaaaatggtttttcaccttgcagATTATTGGTGAAATATCAGTTTCTGGGGCAACATATAAATCCATGGAATTTGTTGGCAGTACTGTTGAAAGTCTGACT

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 6
gtaagcttacaagctgtgttatgtttgttccttcccttaggatctacctgtaaccatgacttcttattcttgttaatcggtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC
              ||||||  | || ||          ||  || ||||||      | | |||||   ||    | |   |  |||||| ||||| |||||  | || || |||||||| |||||||| ||||||||||||||| || |||||||| || | || 
-------------gtgtgtttcgatttttagcaagagctgg--ctccctgtacttg-aagtacttat--atgcgcgttgaggcacacagATCATTGGAGAGATCACTGTTTCCGGTGCAACATACAAATCAATGGAGTTTGTTGGAACAGCTGTAGAACGTATGACG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 6
gtaagcttacaagctgtgttatgtttgttccttcccttaggat---ctacctgtaaccatgacttcttattcttgttaatcggtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC----------------------
                   | ||||||   |||     ||      || ||||||      | | |||||   ||    | |   |  |||||| ||||| |||||  | || || |||||||| |||||||| ||||||||||||||  || |||||||| || | ||                       
------------------gtgtgtttggatctttagcgagagctggctccctgtacttg-aagtacttat--atgcgcgttgaggcacacagATCATTGGAGAGATCACTGTTTCCGGTGCAACATACAAATCAATGGAGTTTGTTGGGACAGCTGTAGAACGTATGACGGTCAGTTCTTTTTCCCCTTACC

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|24764746|gb|CA399909.1|CA399909
EST:     TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAA                         ATTATTGGGGAGATTTCAGTATCTGGTGCAACCTA
genomic: TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTA
EST: gi|32840108|gb|CD979789.1|CD979789
EST:     TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAA                         ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTT
genomic: TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTT
EST: gi|32846022|gb|CD985703.1|CD985703
EST:     TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAA                         ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTT
genomic: TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTT
EST: gi|32840106|gb|CD979787.1|CD979787
EST:     TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAA                         ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTT
genomic: TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTT
EST: gi|211524232|gb|FL397627.1|FL397627
EST:     TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAA                         ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTT
genomic: TAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTT

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: 174

TTCAGGTGCCACCTACTATCAGGTTTGTATTAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

TTCAGGTGCCACCTACTATCAGGTTTGTATTAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

TTCAGGTGCCACCTACTATCAGGTTTGTATTAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 274

TTCAGGTGCCACCTACTATCAGGTTTGTATTAGATGGAGAAATGCCGCCTTATTTACTTGCGAAGGATCTGATTTTGCAAgtaagcttac ... gtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttaggatctacctgtaaccatgacttcttattcttgttaatcggtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC
                                    tgttaat  putative branch site (score: 274)
                             ttattcttgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttacaagctgtgttatgtttgttccttcccttaggatctacctgtaaccatgacttcttattcttgttaatcggtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA