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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgctccttttttttccctttttggttaattttgttttaatgtaacttttatttcaacattctttatccatgttatgctttacttctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG

Basic information

species Zea mays
transcript GRMZM2G044457_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044457_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
gtacgtgctccttttttttccctttttggttaattttgttttaatgtaacttttatttcaacattctttatccatgttatgctttact---tctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG
||| |  |     | |||||   |     |  |||||||||  |  |   | |||||||| | ||||  |   |  || | ||||  |   |   |||| || || ||||         ||||    |||||||||||||||||| ||||||||||| ||||||||  |||| ||||||||||||||||||||||| || ||||||||||| || |||||||||
gtatgcacaa---tcttttctaatgggaatgtattttgtttatacctc-ttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggcttt-------ctggac--ttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG

upper sequence: GRMZM2G044457_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 5
gtacgtgctccttttttttccctttttggttaattttgttttaatgtaacttttatttcaacattctttatccatgttatgctttacttctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG
                  |   | ||||   | |||  | | | || ||||| || | |||   | | | |   | ||||   |   | ||    |    || ||||   |  |           ||||| |||||||| |||||||||||||| |||||||| || || ||||||| ||| || || |||||  ||||||||   ||  | ||||| |||
----------------actgtgtatttgtacactttcatgtcagtgcaacttatactccaatcgtttctttatttcttatatgtctatgctt---tctctatcgcttgttctca---------tgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG

upper sequence: GRMZM2G044457_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 5
gtacgtgctccttttttttccctttttggttaattttgttttaatgtaacttttatttcaacattctttatccatgttatgctttacttctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG
                  |   | ||||   | |||  | | | || ||||| || |     ||  ||| |  || |     | ||| |||   |||    || ||   ||    |   |     ||||| |||||||| ||||||||||||||||||||||| || || ||||||| ||| ||||| |||||  ||||||||   ||  | ||||| |||
------------------tgtgtatttgtacactttcatgtcagtgcaacttatactctccaatcgtttcttaatttc---ttatacgtctatgctt----tttctctcactcgttctca---tgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG

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|88756247|gb|DY540388.1|DY540388
EST:     GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAG                         TCGGATGACCAATGTTGTAATTCTTTGCGAAGAAGTCCGGGAGGC
genomic: GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTT-GCGAAGAAGTCCGGGAGGC
EST: gi|91873243|gb|EB403200.1|EB403200
EST:     GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAG                         TCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
genomic: GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
EST: gi|148944284|gb|EC889380.2|EC889380
EST:     GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAG                         TCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
genomic: GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
EST: gi|50334991|gb|CO530117.1|CO530117
EST:     GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAG                         TCGGATGAACAATGTTGTAATTCTTGCGAAGAAGT
genomic: GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGT
EST: gi|149090670|gb|EE179995.2|EE179995
EST:     GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAG                         TCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
genomic: GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
EST: gi|67035454|gb|CO463987.1|CO463987
EST:     GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAG                         TCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
genomic: GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
EST: gi|149027104|gb|EE046395.2|EE046395
EST:     GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAG                         TCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG
genomic: GGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 77

ATCGAGAGACCATTGCAAAAACATGGAGGAAGGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

ATCGAGAGACCATTGCAAAAACATGGAGGAAGGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

ATCGAGAGACCATTGCAAAAACATGGAGGAAGGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 141

ATCGAGAGACCATTGCAAAAACATGGAGGAAGGCTCGACAAAGGTGAACAATATTGTGGTACGTGTTATGGTGCTGAGGAGgtacgtgctc ... gaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttatgctttacttctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG
         tttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgctccttttttttccctttttggttaattttgttttaatgtaacttttatttcaacattctttatccatgttatgctttacttctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG