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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggccgatactatccatttacagagttcagatgctgttgaaggatatgcacatattttaccatgatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT

Basic information

species Zea mays
transcript GRMZM2G079538_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 8
gtaaggccgatactatccatttacaga--gttcagatgctgttg-----aaggatatgcacatattttaccatgata--ttgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT
|||||  | |   |   |||  | ||   |  |||||  | ||      | | | | ||| || ||| |||||  ||  ||||||||||||||||||||||||||||||||||||||||||||| | |||||||| || ||||| |||||||||||||  ||||||||||||||||||||
gtaagatcaactttcatcatcaataggttgcacagatttttttttttacaggtacaagcatatctttaaccattttaatttgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTTTGAAGGATTCACAAAACACATTTGCAATGCTGACCACATTTAATGAAGTTGACAT

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------------------------------------------------------------------------gtaaggccgatactatccattt---acagagttcagatgctgttgaaggatatgcacatattttaccatgatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT
                                                                                                          |  ||         ||  |||   ||  ||||||||| ||| ||    | ||      |  |||   |  |||||||||| || ||| ||||  | ||||| ||| ||||||  ||| | || |||||||| ||||| |||||||||||||  ||||| ||||||||||| ||
gtaagcatcatgaacttaattatttattaaaatatacctgtaatcctgtctgttaggggttctgtaaaattactatattccacttcatttgagggagggagctggatgggggttgagtggtctgtttcttactaagttcagatcctggtgctaca-atatttggaacttattct--tattgcagGTTCCTATGACAAGATTAAGGAAACGTGTTGCAACACGTTTGAAAGATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT
















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|211169880|gb|FL077609.1|FL077609
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|5343075|gb|AI795485.1|AI795485
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCC
genomic: AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCC
EST: gi|13558100|gb|BG549456.1|BG549456
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|211169873|gb|FL077602.1|FL077602
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|32801408|gb|CD953644.1|CD953644
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTA
genomic: AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTA
EST: gi|32801064|gb|CD953300.1|CD953300
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTA
genomic: AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTA
EST: gi|7145229|gb|AW506710.1|AW506710
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
EST: gi|13558537|gb|BG549893.1|BG549893
EST:     AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGG                         GTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT
genomic: AAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCT

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: 44 (upstream exon), 48 (downstream exon)
Score: 102

AAAAGTAGATCCTCCCAAGATGCAAGCACCAAAGCCAACTGCACCATCAAAAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

AAAAGTAGATCCTCCCAAGATGCAAGCACCAAAGCCAACTGCACCATCAAAAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

AAAAGTAGATCCTCCCAAGATGCAAGCACCAAAGCCAACTGCACCATCAAAAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

AAAAGTAGATCCTCCCAAGATGCAAGCACCAAAGCCAACTGCACCATCAAAAACATCCCCTTCAGAACCACAGCTCCCTCCAAAAGAACGAGAGCGGCGGgtaaggccga ... gatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagagttcagatgctgttgaaggatatgcacatattttaccatgatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT
                               acatatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggccgatactatccatttacagagttcagatgctgttgaaggatatgcacatattttaccatgatattgcagGTGCCAATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG