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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttttcttaattgcttctgcacggccgtacaccaaccttccaatctaataacagctgggcccttggttgtgttcctacttactactgattgtaataatgaatttaatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 5
gtctgttttcttaattgcttc---tgcac--ggccgtacaccaaccttccaatct----aataacagctgggcccttggttgtgttcctacttactactgattgtaataatgaatttaatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
|| ||||| || |  || ||    |||||  ||   | |||  |  |     | |    |||  ||       |      |    |  |||    ||||||||||||| || ||     | |  ||||||||||||| |||||||||||||| || ||| | ||    ||||| ||   ||||||||| |||||||| ||||||||||| ||||||||||| || |
gtgtgtttcctaatgtgatttgtgtgcactgggagcttcactgatatatacgtattccaaattccattaacaacaaacactaaccttttacactttactgattgtaatgatcaacc--gtgtgtagGATTCATCTGGCATATTCTGGGATAACGATAGTTTGGCCAGACTGTTAGCGCAAGAACTTAAAGCTGATCTCCTTATCATGCTCAGTGATGTGGAGGGGC

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 2
gtctgttttcttaattgcttctgcacggccgtacaccaaccttccaatctaataacagctgggcccttggttgtgttcctacttactactgattgtaataatgaatttaatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
                |  | |  |     | |   | ||||   |  ||      |  ||   || |   | | |    |  |||  |   |   | ||| | |||| || | |||||||| ||||||||||| ||||||||||| ||| || | |||||||||||    ||  | || || ||||||||| |  || | |||||||| ||||| |
----------------gaatgtttagtttggaattgctacctggaatacttgcttta-ttgtttccatttctatctattcaagtacatcaagtgtcattaacgtattttatgtgcagGATTCTTCTGGTATATTTTGGGATAATGATAGTTTATCTGCTCTGTTGGCCTTGGAGTTAAAAGCCGATCTTCTTGTTTTGTTGAGTGATGTAGAAGGTC

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 2
---------gtctgttttcttaattgcttctgcacggccgtacaccaaccttccaatctaataacagctgggcccttggttgtgttcctactt---------actactgattgtaataatgaatttaatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
          | |  || |  || |  | ||    |    |  |    | ||    |||  ||  |  ||     ||| || | ||| |  |          | || |   | |||     |      | | |||||||| ||||||||||||||||| ||||||||| | || | ||| |||||    |||||||| ||||| || ||| |  |  | |||||||| || || |
gtaagctgcttttccttacacaaattttcctttgtgaaaatttagtctcttttatttctcctagaaaatgttagtttgattttcttcgtcttgtgacgttaaattattacctttaagggcaagaactgtctgcagGATTCTTCTGGTATATTCTGGGACAATGACAGTTTGGCTGGTCTATTGGCTCTGGAACTTAAAGCTGACCTCCTTGTTCTATTGAGTGATGTTGAGGGTC

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G41850.1 (Glycine max), 3'ss of exon 2
gtctgttttcttaattgcttctgcacggccgtacaccaaccttccaatctaataacagctgggcccttggttgtgttcctacttactactgattgtaataatgaatttaatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
              || ||| | || |   | |     |  ||  | |       ||  |    ||     | | |   ||  |||  |   |   | ||| |  |||  | | |||||||| ||||||||||| ||||||||||| ||| || | |||||||||||    ||  | || || ||||||||| |  || | |||||||| ||||| |
-------------ttttcttttcca-gattgaaagtttagtttgaagtt--gctgca-ttctttccagttctatatatttaagtacatcaagtgtcattaacgttttttttgtgcagGATTCTTCTGGTATATTTTGGGATAATGATAGTTTATCTGCTCTGTTGGCCTTGGAGTTAAAAGCCGATCTTCTTGTTTTGTTGAGTGATGTAGAAGGTC

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 5
---------------------------------------gtctgttttcttaattgcttctgcacggccgtacaccaaccttccaatctaataacagctgggcccttggttgtgttcctacttactactgattgtaataatgaatttaatt-tacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
                                          |  | |   |  || ||       ||  | ||||    |   ||   || ||||| ||     |  |    |   |||   | |||| |  ||   | | |||    || | |||||||| ||||| ||||| ||||||||||||||| || ||||| | ||||||   ||| | || ||||||||||||||  || | |||||||| || || |
gtttgttattctacttgtctggtttgttatcagagcagaacttaatcttagagctgattgcttcaagctatgcacc--tttataaaaaaaaaaacaggtgacgtatgagactag--actagagaatacttaaagtgtcactaaatcattttatgcagGATTCTTCTGGCATATTTTGGGATAATGACAGTTTATCAGCTTTATTGGCATTGGAATTAAAAGCTGATCTTCTTATTTTGTTGAGTGATGTAGAGGGTC

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------gtctgtt-ttcttaattgcttctgcacggccgtacacca--accttccaatctaataacagctgggcccttggttgtgttcctacttacta-ctgattgtaataatgaatttaa---tttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
                                                         ||  |   || | ||  | | ||    | | |||||  |  |   |  |||| | |||   |   |  | |     | ||      ||||| || |  |    | || | || |   | ||||||||||  |||||||||| ||||||||||||||  |||| |||||  || |   ||| || || ||||||||| | ||  | || |||||||| || || |
gtttgttgattgcctttcttttgctctttgacatagagttctactaactttggagatgtgagaaattgtaaagcgatacttattgactgtacatgatgaaactagaatcaagtaatttcctagttcctctgaatcttttagtctactaacttacagcttcactgtacttcaacgtatacagGATTCTACTGGTATATTTTGGGATAATGACAGCTTAGCCGCTCTTCTGTCGCTAGAGCTGAAAGCTGATCTTTTGATTCTTCTAAGTGATGTTGAGGGCC

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 5
gtctgttttcttaattgcttctgcacggccgtacaccaaccttccaatctaataacagctgggcccttggttgtgttcctacttactactgattgtaataatgaatttaatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
        | ||| ||  || |  |      |  |  |   || || |  | |    |||    | |  ||  | | ||   |   ||     | | || |||||     ||| |||||||| ||||||||||| || |||||||||||||| ||| ||||  ||||    ||||| || ||||| |||||| || || | |||||||| || || |
-------ctattatttatttatttat-----tttattatttttgcacttcagtt---gctta--cttatgtcatttgccagatgtatatgttgtctgattatgaaaactgttttcagGATTCTTCTGGTATATTTTGTGATAATGACAGTCTGGCAACTCTACTGGCTCTGGAACTAAAAGCTGACCTTCTTGTCTTGTTGAGTGATGTAGAGGGTC

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|211514098|gb|FL183141.1|FL183141
EST:     CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAG                         GATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
genomic: CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
EST: gi|6021065|gb|AW065993.1|AW065993
EST:     CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAG                         GATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
genomic: CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
EST: gi|149066720|gb|EE286861.2|EE286861
EST:     CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAG                         GATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
genomic: CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
EST: gi|74245732|gb|DT653646.1|DT653646
EST:     CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAG                         GATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
genomic: CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
EST: gi|101391687|gb|EB817780.1|EB817780
EST:     CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAG                         GATTCATCTGGTATATTCTGGGGATA-TGACAGTCTAGCAGCT
genomic: CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGG-ATAATGACAGTCTAGCAGCT
EST: gi|211514099|gb|FL183142.1|FL183142
EST:     CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAG                         GATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA
genomic: CCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCA

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 72

GGACCAGCTCCGTGAGACTGTTTTTTCACTGTTAGATCTTAAAGTAGTACCCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 10

GGACCAGCTCCGTGAGACTGTTTTTTCACTGTTAGATCTTAAAGTAGTACCCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 270

GGACCAGCTCCGTGAGACTGTTTTTTCACTGTTAGATCTTAAAGTAGTACCCTTATTTAATGAGAATGATGCCATCAGTACCCGGAGACAGCCATATGAGgtctgttttc ... taatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccttggttgtgttcctacttactactgattgtaataatgaatttaatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC
                        tactgattgtaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttttcttaattgcttctgcacggccgtacaccaaccttccaatctaataacagctgggcccttggttgtgttcctacttactactgattgtaataatgaatttaatttacagGATTCATCTGGTATATTCTGGGATAATGACAGTCTAGCAGCTCTGTTGGCAGCAGAACTTAATGCTGATCTTCTTATCATGCTTAGTGATGTGGAAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG