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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtctaaacgatacatcttcag

Basic information

species Zea mays
transcript GRMZM2G152127_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 5'ss of exon 16
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaa---cagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtc-----taaacgata-catcttcag
|||||| |||||||||||||||||||||||||| || ||||| || || || || |||||| |||||||||| || |||||| |||||| |||||||||||||||     | |    ||  ||||| | | ||       | |||      ||  | |   |  |      ||  |      || | ||     ||   || |   ||| |||
CATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAATTTGGAGAACATATTCGGTCAAGCTCCTGGTGTTGATTCGgtacaatctgataacctagctttcatttgctcaaaaccttttttccattataaccgatcttacgtttccatatgttgacatgctgactcgccgttatttgacaatctctccag

upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
lower sequence: AT1G64400.1 (Arabidopsis thaliana), 5'ss of exon 14
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtac-agctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtctaaacgatacatcttcag
||| ||||| |||||||||||||| || || || || ||||| |||||||| ||||||||  |||||||||| |   ||||     | ||  |||| ||||||  || | |||| |      | ||    ||  |||  |||    |  |  | | |   ||| ||    |||  ||| |   ||                    
CATCGACCGTAAGAAGAACATCTTTAAACTGTCTCAAGGAGAATACGTTGCCGTTGAGAACTTGGAGAACATATACAGTCATGTCGCCGCCATTGAATCGgtattagttgaaaata-----taactcttaag--taaccgttacataaaacttagct---aatgatctgttaaaacattttgcag--------------------

upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtctaaacg-atacatcttcag
 || ||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||||||  |||| ||||| | |||||    | ||| | |||| ||||||   |||  ||  || |     |||    |    |  ||   ||     |  || |   | |||   |  | | ||||| ||| | |  |  ||   ||    
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattt--tggttc-tctctcagtttcattgtgtatgcctct--

upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
lower sequence: EDO95646 (Chlamydomonas reinhardtii), 5'ss of exon 1
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttc-tgcagcaaatggttacaaataattccataatccatctctaagtctaaacgatacatcttcag
           | |    |||| | | || |||    |      |  | | ||     ||   | ||||||||||    |  |  |  | ||  | | |||            | |      |  |    |  |  |||  | || || | |     | |     |       |     |    || | ||              
----------GACATCGCCATCCTGACGCCCTCGGGCGCCATCAAGATCGTGGACCGCAA---GAAGAACATCTTCAAGCTCAGCCAGGgtg--ggtgcggggagagggtgtgcggggggggtggaggaggcgtgggtgggcgtggaggagacatggagatggggtgggggttttaggattgtggtttgaa--------------

upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
lower sequence: EDO96800 (Chlamydomonas reinhardtii), 5'ss of exon 13
--------------------------------------------------------------CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTAC--GTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACT--CCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattcc-ataatccatctctaagtctaaac--gatacatcttcag-------------------
                                                              ||| |||||||||||||||||||||||||||   ||||| | |||   | ||||  ||     |||  |   ||     |    |||  ||   | |  | || |  | || |||    |         |  ||      | | | ||     | | |       |    |  | | ||   ||||  ||| |  |  |   |  | || |                   
GCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCAGGgtgcgtaatggctgcgtatgcatggctgccgcgaattaggagctcgacttgccgtgtatacactccgggcggcacaagcggggagctcggcaggcacgagtggcgatgtgtgctgacttgcattgtgttgccctgacactcggcctctgtgtcaaccctggccccggcgtctgccattgccgtgtgccccag

upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtctaaacgatacatcttcag---
 ||||| ||||||||||||||||||||||| || || ||||| |||||||| || || || || || ||  | |    | |  |  |  |||||||| |||||        | || | | |   |   | ||  |  |  |||    |        |||   | | |  ||    || || |  ||||  |  | |      ||   
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatgagc---atcactttacgattctgctgttca--taatctagttcttgcaaccacatgcactgctttagcagatttcga--tctacccatttcggtactaggtt

upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
lower sequence: PP1S218_19V6.1 (Physcomitrella patens), 5'ss of exon 17
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtac---agctcaaaacagtcttcatct---acacagtctaagtgttctgcagcaaatggttacaaataattccataatc-catctctaagtctaaacgatacatcttcag---------------------------------------------------------------------------------
||| ||| | |||||||||||||||||| | |||||||| || |||||||| || ||||| || ||||  || | |||||||  |   ||| | |||  ||||    ||||   | |||   |   ||   ||   ||  ||      | |  |   || ||||    |  |  || | |   |  | || |||   | |  | |    ||                                                                                 
CATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAACCTTGAGAGTATTTATGGTCAATGTGAAGCTATCGATCAGgtattagagctgtgaccagctcttgcctctcactatgttcaacatcatttccacgtttgtttactc-caggttaatgaccatgtgccaaaatcttctctagccttgcaaagctttactgattacttggggtagtagctcattttgcgctacttatatgtgacagtgaactgattagtactttcattgatcag

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|71768490|gb|DR966427.1|DR966427
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|33096859|gb|CF056819.1|CF056819
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|86470254|gb|DY236624.1|DY236624
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|33770959|gb|CF273253.1|CF273253
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|211196583|gb|FL038431.1|FL038431
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|71426982|gb|DR808032.1|DR808032
EST:     CGGCTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|60349126|gb|DN216099.1|DN216099
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|60339626|gb|DN206599.1|DN206599
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|6020548|gb|AW065476.1|AW065476
EST:     CGGTTGANAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGNTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|60358314|gb|DN225287.1|DN225287
EST:     GGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: GGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|94473569|gb|EB702527.1|EB702527
EST:     GGGTTGGGAATTTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTTTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: -GGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|74246154|gb|DT654068.1|DT654068
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|74239652|gb|DT647566.1|DT647566
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|16920190|gb|BM074544.1|BM074544
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAAC
EST: gi|211444856|gb|FL116921.1|FL116921
EST:     CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCG                         ATTTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCA
genomic: CGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTT-GGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCA

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: 46 (upstream exon), 49 (downstream exon)
Score: 229

CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAACCCCAACACACAAGCACTGGAGCGCTGGGCAGAGTCGAACGGGGTAACTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 94

CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAACCCCAACACACAAGCACTGGAGCGCTGGGCAGAGTCGAACGGGGTAACTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 82

CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAACCCCAACACACAAGCACTGGAGCGCTGGGCAGAGTCGAACGGGGTAACTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 298

CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctca ... acatcttcagATTTGGGTCTACGGCAACAGCTTCGAGTCGAGCCTGGTAGCAGTTGTGAACCCCAACACACAAGCACTGGAGCGCTGGGCAGAGTCGAACGGGGTAACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtctaaacgatacatcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT