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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagaaaccccctagttattttgctgcactaacatttttctggtaaaaaatacttaggtttgagttttcaatctcctgttgtgatttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAACTAACAACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTGATGG

Basic information

species Zea mays
transcript GRMZM2G036872_T01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036872_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os07g46450.1 (Oryza sativa), 3'ss of exon 21
gtaagagaaaccccctagttattttgctgcac----taacatttttctggtaaaaaatac-----------ttaggtttgagttttcaatctcctgttgtgatttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAACTAACAACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTGATGG
||||  ||||  ||   | |      ||| |         | | |     |||| |  ||           ||   |  |||| ||||||   ||  | | | |  || ||||| ||||| || ||||| |   |  | ||| | || ||||||||||| ||||| || |||||||||||||||||||||||||||||||||||||| ||||
gtaaaggaaaaaccactgcttccgaactgaagggtgcggtagtgtcgaaataaagaccacaccgcttctcattcaatacgagtattcaattctcttgtatcactatca-cagGGCGTCGAGTACGGGAGGCAAGCTCCCGTGGCATCGTCCACTCTGGTCGAACTGACGACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTAATGG
















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|37391484|gb|CF632985.1|CF632985
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|37391484|gb|CF632985.1|CF632985
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|18965228|gb|BM661464.1|BM661464
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAA                         C
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAAgtaagagaaa ... tttgcagcag-
EST: gi|18965228|gb|BM661464.1|BM661464
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAA                         C
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAAgtaagagaaa ... tttgcagcag-
EST: gi|18965228|gb|BM661464.1|BM661464
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAA                         C
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAAgtaagagaaa ... tttgcagcag-
EST: gi|60356361|gb|DN223334.1|DN223334
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|60356361|gb|DN223334.1|DN223334
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|89247359|gb|DY619145.1|DY619145
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAA                         GGTGTCGAATATGGGAGACCGCCCTCTGTGTCGTCATCCACTCTGGTTGAA
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAAgtaagagaaa ... tttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAA
EST: gi|60337955|gb|DN204928.1|DN204928
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|60337955|gb|DN204928.1|DN204928
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|16926041|gb|BM079109.1|BM079109
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|16926041|gb|BM079109.1|BM079109
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|18167769|gb|BM337609.1|BM337609
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca
EST: gi|18167769|gb|BM337609.1|BM337609
EST:     TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAACA                        
genomic: TGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACG-AA-Agtaagagaaa ... tttgcagca

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: 33 (upstream exon), 38 (downstream exon)
Score: 10

TTTCTCCCGAAAGCATTCCTCGGACACCTCCTTGAGTGATTCTACAAGTGTGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAAgtaagagaaa ... tttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAACTAACAACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTGATGG


Block sizes: 44 (upstream exon), 34 (downstream exon)
Score: 10

TTTCTCCCGAAAGCATTCCTCGGACACCTCCTTGAGTGATTCTACAAGTGTGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAAgtaagagaaa ... tttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAACTAACAACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTGATGG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 11

TTTCTCCCGAAAGCATTCCTCGGACACCTCCTTGAGTGATTCTACAAGTGTGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAAgtaagagaaa ... tttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAACTAACAACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTGATGG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 8

TTTCTCCCGAAAGCATTCCTCGGACACCTCCTTGAGTGATTCTACAAGTGTGCCTGCAGAGGGCGGGCCAATGTTGGTGAACATCCCTAGAACAACGAAAgtaagagaaa ... tttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAACTAACAACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTGATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtaaaaaatacttaggtttgagttttcaatctcctgttgtgatttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAACTAACAACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTGATGG
     aaaaaatactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagaaaccccctagttattttgctgcactaacatttttctggtaaaaaatacttaggtttgagttttcaatctcctgttgtgatttgcagcagGGTGTCGAATATGGGAGACCGCCGTCTGTGTCGTCATCCACTCTGGTTGAACTAACAACCAGGCTAGATTTCTTCAAAGAACGGCGGTCACAATTGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC