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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcatacttccttccactttctgtaactacggataacctctgttttatacacacatgaatgaaaatgctggtcacatagttgccggacagctgatgtaccgaaccgctcgtacttaacttgctgcag

Basic information

species Zea mays
transcript GRMZM2G114126_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 8
AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcatacttccttccactttctgtaactacggataacctctgttttatacacacatgaatgaa-aatgctggtcacatagttgccggacagctgatgtaccgaaccgctcgtact-taacttgctgcag
|||||||||||||||||| || || || |||||| ||||  |||| || || ||||| || ||||||||||| ||||||||||| || ||||| ||||||||  |    | || ||||   | ||  | | |||  | ||| | |||| |||| |  ||    | |  ||| ||  |   |||  ||  ||| | ||    |  | |  |      | | ||  |||   |||
AGAACCCAAAATAATGATAACTGGAAAGTGGAACCAGTCCATGAGTTGTCAGCCATGCGATCAAGAAGGCGATCCTCTTCCAGGAACTGAGCTAAAGGAGgtcag----aatttcttcggatgtccattattacacagaacatttgttatataaaggcaaagctaattaatacttctataataactgt-ggatatct----tctcaactcttcaacattatactttgtcccag

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT5G02100.1 (Arabidopsis thaliana), 5'ss of exon 8
AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcatacttccttccactttctgtaactacggataacctctgttttatacacacatgaatgaaaatgctggtcacatagttgccggacagctgatgtaccgaaccgctcgtacttaacttgctgcag
||| ||||| ||  | || || || ||||||||| ||||  |||| |  || ||||||||    |||||||| |||||||||||||| || ||||||||||||      | |||  ||| ||      |||       |  || | | |  |   ||| |   | |  ||| |  |  || ||                                                
AGAGCCCAAGATGCTAATGACCGGAAAATGGAACGAGTCCTTGAGTTATCAGCCATGTGATGCGGAAGGCGAACCTCTTCCAGGCACCGAACTGAAGGAGgttttatcaatttctctcctctaagca-aaccctctgcatactatatctagt---cacctttctaattatgttacttccacag------------------------------------------------

upper sequence: GRMZM2G114126_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 8
AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcatacttccttccactttctgtaactacggataacctctgttttatacacacatgaatgaaaatgctggtcacatagttgccggacagctgatgtaccgaaccgctcgtacttaacttgctgcag
 |||||||||||| |||| ||||||||||||||  ||||| |||| | |||||||||||||   ||||| || |||||| ||||||| || ||||||||||||  ||  | |   ||    ||||  ||  |   | |    |     | | | |    ||  |  | ||  | |  | |  | ||||   || |||||     |||||                      
GGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctcattgaatttagttttcattatttgttgttg---tgcaagtcaaatattgttgctt--atattttagctagaatgctgccatgca-ctgat---ttgaacc----------------------

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|211454957|gb|FL196641.1|FL196641
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATATGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTACCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|74236528|gb|DT644442.1|DT644442
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|60356147|gb|DN223120.1|DN223120
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|67022184|gb|CO450933.1|CO450933
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|61118185|gb|DN559146.1|DN559146
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|78120438|gb|DV538822.1|DV538822
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|60396557|gb|DN229426.1|DN229426
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|67032806|gb|CO461555.1|CO461555
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|71759542|gb|DR957479.1|DR957479
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATTTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
EST: gi|8367795|gb|BE050740.1|BE050740
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTTGCCCCTGCCCCACAGAACGACGGGTATCA
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCA
EST: gi|14243772|gb|BG841435.2|BG841435
EST:     AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAG                         ATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC
genomic: AACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACAC

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: 223

AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACACTTTGCGCACAAAATAAACAGCTTCAGCACGGCACCTAAGAAGCTGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 768

AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACACTTTGCGCACAAAATAAACAGCTTCAGCACGGCACCTAAGAAGCTGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 852

AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACACTTTGCGCACAAAATAAACAGCTTCAGCACGGCACCTAAGAAGCTGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 392

AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcata ... cttgctgcagATCTGGAGAGTCGCCCCTGCCCCACAGAACGACGGGTATCAGTACACACACTTTGCGCACAAAATAAACAGCTTCAGCACGGCACCTAAGAAGCTGTTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCATGTGACCAAGAAGGCGACCCTCTTCCAGGCACGGAGCTGAAGGAGgttggtcatacttccttccactttctgtaactacggataacctctgttttatacacacatgaatgaaaatgctggtcacatagttgccggacagctgatgtaccgaaccgctcgtacttaacttgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG