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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactttggtcactgagtctatgtaccctgtcttttggatttgctttttgtcactgtttccatcaatgtggtcttgatatattagcttttccatat...

Basic information

species Zea mays
transcript GRMZM2G423861_T01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 22
TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactttggtcactgagtctatgtaccctgtcttttggatt-tgctttttgtcactgtttccatcaatgtggtcttgat--atattagcttttccatat-------
|||| |||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||| |||||||||||||||| || || ||||||| | ||   |  ||    |  | |||      |||||  || |||   | ||    || | || |  |   || ||||     |||   ||| |   ||       
TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaatttctattgct---ccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtattgactggcattttttttcctccatcttgcag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 21
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 5'ss of exon 24
TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtact---ttggtcactgagtc-tatgtaccctgtctt----ttggatttgctttttgtcactgtttc-------catcaatgtggtcttgatatattagcttt---tccatat---------------------------------------
|||||||||| |||||||| || || |||||||||||| | |||||||| ||| | |||||||||||||||||  |||| |||||  | || || ||   ||  | |      |  |   |||||| | |     |  |  |    ||  ||||| | ||| ||  |  | |        |  || | ||| |  |   |||||   |   | | ||                                        
TGCTTATGAGCGATTCTCTCGGTGGAAATGCGAAGACCCTCATGTTTGTAAATATCTCACCAGCAGAGTCTAATCTGGACGAGACCCATAATTCACTCTGgtgaggaacggactatttcttgagtcctgtcagttcactactaaaattcaatttgatgtttctcgatactccagagaggtaagaagggggtttccagtcattagtgataagtacgtagtgatttttttgattgacctttattgttggtgtattgtag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 21
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 23
TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt----tggtcactgagtctatgta--------ccctgtcttttggatttgctttttgtcactgtttccatcaatgtggtcttgatatattagcttttccatat-----------------------------------------------------------------
|||| ||||| |||||||| || || |||||||||||  | |||||||| ||| | ||||| |||||||| ||| |||| |||||  | || || ||   ||  |||  |    |||    ||   || |  |        |  | | ||||   ||  |||||  |  || |       |||   |  |  | | ||     |||| | ||                                                                 
TGCTCATGAGCGATTCTCTTGGTGGAAATGCGAAGACACTCATGTTTGTAAATATCTCACCGGCAGAGTCCAACCTGGATGAGACCCATAATTCACTCTGgtgagtaactgatctggctcgtgttcctttccaatttttatctttattttttcacttcacttttgatgtctctagattctaataaaggttcaa-agatggagatttctagatgtatgagttgatttgatttccagcctgaaaatgcttacttctgacttctgttgttgtattggtag

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|211369815|gb|FL432853.1|FL432853
EST:     AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGAT                         GTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
genomic: AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
EST: gi|60396505|gb|DN229374.1|DN229374
EST:     AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGAT                         GTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
genomic: AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
EST: gi|78025391|gb|DV493778.1|DV493778
EST:     AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGAT                         GTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
genomic: AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
EST: gi|67014388|gb|CO443137.1|CO443137
EST:     AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGAT                         GTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
genomic: AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
EST: gi|211378041|gb|FL328240.1|FL328240
EST:     AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGAT                         GTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC
genomic: AATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGC

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: 47 (upstream exon), 43 (downstream exon)
Score: 43

TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGCTCCAAAAGAAATCATGAGATTGAAGAAGTTGATCGCCTACTGGAAGGAG


Block sizes: 47 (upstream exon), 13 (downstream exon)
Score: 2

TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGCTCCAAAAGAAATCATGAGATTGAAGAAGTTGATCGCCTACTGGAAGGAG


Block sizes: 48 (upstream exon), 32 (downstream exon)
Score: 3

TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGCTCCAAAAGAAATCATGAGATTGAAGAAGTTGATCGCCTACTGGAAGGAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 35

TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactt ... acccttgtagGTATGCTTCACGCGTTCGATGCATTGTTAATGATACGAGCAAGCATGTTGCTCCAAAAGAAATCATGAGATTGAAGAAGTTGATCGCCTACTGGAAGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactttggtcactgagtctatgtaccctgtcttttggatttgctttttgtcactgtttccatcaatgtggtcttgatatattagcttttccatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT