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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttctgcagtgatgacgtttcttgataaattgtcatgcattatgttgacatgatttgagccggatgatttgtattttaaagtatcctatgcttgcag

Basic information

species Zea mays
transcript GRMZM2G174797_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174797_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g03530.2 (Oryza sativa), 5'ss of exon 6
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttc-------tgcagtgatgacgtt------tcttgataaattgtcatgcattatgttgacatgatttgagccg-gatgatttgtattttaaagtatcctatgcttgcag
||||||  || ||||| || | | ||||||||||||||||||| |||||||| ||||||||||||||||||||||| || |||||| | || ||||||||||||  |||          ||| ||||  ||      | |  ||||  ||||||||||| | |  |||    |||| ||  ||  | |  | |||| ||||               
TTTGGAGATTAGCTTATCCCAGCCGACAACTTCCTCCTCTGAAATCAGATCTATGGAAGGAGATGGGCTGGCAGAATTCTGATCCAGCAACTGATTTTAGgttcgtttcgctaatccctagtaatgattttaggatatatatataagctgtcatgcatt-tatcaacaccgcttgaacctcgacaactaatcttttgaagt---------------

upper sequence: GRMZM2G174797_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g03530.3 (Oryza sativa), 5'ss of exon 8
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttc-------tgcagtgatgacgtt------tcttgataaattgtcatgcattatgttgacatgatttgagccg-gatgatttgtattttaaagtatcctatgcttgcag-----
||||||  || ||||| || | | ||||||||||||||||||| |||||||| ||||||||||||||||||||||| || |||||| | || ||||||||||||  |||          ||| ||||  ||      | |  ||||  ||||||||||| | |  |||    |||| ||  ||  | |  | |||| |||||||  ||||||||||     
TTTGGAGATTAGCTTATCCCAGCCGACAACTTCCTCCTCTGAAATCAGATCTATGGAAGGAGATGGGCTGGCAGAATTCTGATCCAGCAACTGATTTTAGgttcgtttcgctaatccctagtaatgattttaggatatatatataagctgtcatgcatt-tatcaacaccgcttgaacctcgacaactaatcttttgaagtatctaatgcttgcagagcag

upper sequence: GRMZM2G174797_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g03530.1 (Oryza sativa), 5'ss of exon 8
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttc-------tgcagtgatgacgtt------tcttgataaattgtcatgcattatgttgacatgatttgagccg-gatgatttgtattttaaagtatcctatgcttgcag
||||||  || ||||| || | | ||||||||||||||||||| |||||||| ||||||||||||||||||||||| || |||||| | || ||||||||||||  |||          ||| ||||  ||      | |  ||||  ||||||||||| | |  |||    |||| ||  ||  | |  | |||| |||||||  ||||||||||
TTTGGAGATTAGCTTATCCCAGCCGACAACTTCCTCCTCTGAAATCAGATCTATGGAAGGAGATGGGCTGGCAGAATTCTGATCCAGCAACTGATTTTAGgttcgtttcgctaatccctagtaatgattttaggatatatatataagctgtcatgcatt-tatcaacaccgcttgaacctcgacaactaatcttttgaagtatctaatgcttgcag

upper sequence: GRMZM2G174797_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g03270.1 (Oryza sativa), 5'ss of exon 6
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct----------gcagtgat-----gacgtttcttgataaattgtcatgcattatgttgacatgatttgagccg-gatgatttgtattttaaagtatcctatgcttgcag
||||||  || ||||| || | | ||||||||||||||||||| |||||||| ||||||||||||||||||||||| || |||||| | || ||||||||||||  |||           | | ||||     ||  | | |  ||||  ||||||||||| | |  |||    |||| ||  ||  | |  | |||| |||||||  ||| ||||||
TTTGGAGATTAGCTTATCCCAGCCGACAACTTCCTCCTCTGAAATCAGATCTATGGAAGGAGATGGGCTGGCAGAATTCTGATCCAGCAACTGATTTTAGgttcgtttcgctaatccctagtaatgattttaggatatatatatataagctgtcatgcatt-tatcaacaccgcttgaacctcgacaactaatcttttgaagtatctaatgattgcag

upper sequence: GRMZM2G174797_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv14s0006g02040.t01 (Vitis vinifera), 5'ss of exon 1
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgtt--cagttctgcagtgatgacgtttcttgataaattgtcatgcattatgttgacatgatttgagccggatgatttgtattttaaagtatcctatgcttgcag
||||||| || ||||| |||   ||  | || ||  |||| |||||||| ||||||||||||||||| |||||     | ||||  || |||||||||||||    ||      |   || |   |     ||  |  | | |   ||||||| |  ||  || |   | ||      |  || ||   ||  ||         
TTTGGAACTTAGCTTATCCTGGTAGGGAGCTCCCCTCTCTTAAGTCAGAGCTCTGGAAGGAGATGGGTTGGCAAGGTACTGATCATTCGACAGATTTTAGgtgggtagaggactatatataaacatctggtatttacagacttctcttatgttcatgtgtattaatgtgaatt-----tggttaaacacattttag--------

upper sequence: GRMZM2G174797_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv08s0056g00790.t01 (Vitis vinifera), 5'ss of exon 6
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttca------gttctgcagtgatg-acgtttcttgataaattgtcatgcattatgttgacatgatttgagccggatgatttgtattttaaagtatcctatgcttgcag
| ||||  || ||||| |||   ||  | || ||  |||| |||||||| ||||||||||||||||| |||||     | ||||| || |||||||||||||           | | ||   |   | | |  ||    | || ||     ||    ||   | || |||    | | |     ||||||                   
TCTGGAGCTTAGCTTATCCTGGTAGGGAGCTCCCCTCTCTTAAGTCAGAGCTCTGGAAGGAGATGGGTTGGCAAGGTACTGATCCTTCGACAGATTTTAGgtgggtagaggactatacataaacatatggtatttacagacttctctcatgttcatgtgtattaatgtgaatttggtcacacacattttag------------------

upper sequence: GRMZM2G174797_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0047g00160.t01 (Vitis vinifera), 5'ss of exon 1
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttc----agttctgcagtgatgacgtttcttgataaattgtcatgcattatgttgacatgatttgagccggatgatttgtattttaaagtatcctatgcttgcag
| ||||  || ||||| |||   ||  | || ||  |||| |||||||| ||||||||||||||||| |||||     | ||||| || | |||||||||||      ||  ||  | |    || | |  |  |  |  | | |   | ||||| |  ||  || |   | ||      |  |  ||   ||  ||         
TCTGGATCTTAGCTTATCCTGGTAGGGAGCTCCCCTCTCTTAAGTCAGAGCTCTGGAAGGAGATGGGTTGGCAAGGTACTGATCCTTCAATAGATTTTAGgtgggtagaggactata-tataaacatctggtattttacagacttctctcatgttcatgtgtattaatgtgaatt-----tggtcaaacacattttag--------

upper sequence: GRMZM2G174797_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0096g00560.t01 (Vitis vinifera), 5'ss of exon 1
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTA----Ggttcagttctgcagtgatgacgtttcttgataaattgtcatgcattatgttgacatgatttgagccggatgatttgtattttaaagtatcctatgcttgcag
||||||  || ||||| |||  |||  | || ||  |||| |||||||| ||||||||||||||||| |||||       ||||| || ||||||||||    |||  ||  ||  | |    || | |  |  | |  |  | |   | ||||| |  ||  || |   | ||      |  |  ||   ||  ||         
TTTGGAGCTTAGCTTATCCTGGCAGGGAGCTCCCCTCTCTTAAGTCAGAGCTCTGGAAGGAGATGGGTTGGCAAGGTATTGATCCTTCAACAGATTTTAAgtgggtagaggactata-tataaacatctggtatttacata-cttctctcatgttcatgtgtattaatgtgaatt-----tggtcaaacacattttag--------

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|76294108|gb|DV033676.1|DV033676
EST:     CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAG                         AGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
genomic: CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
EST: gi|71433002|gb|DR814052.1|DR814052
EST:     CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAG                         AGCAGCTGGGTTCATGTCCTTGGAGAATTTAATATATTTTGCCAGAAATTA
genomic: CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
EST: gi|31664136|gb|CD573316.1|CD573316
EST:     CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAG                         AGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
genomic: CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
EST: gi|71433003|gb|DR814053.1|DR814053
EST:     CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAG                         AGCAGCTGGGGTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAA
genomic: CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAA
EST: gi|71757287|gb|DR955224.1|DR955224
EST:     TTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAG                         AGCAGCTGGGTTCATGTCCTTGGAGAATTTAATATATTTTGCCAGAAATTA
genomic: CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
EST: gi|78116832|gb|DV535219.1|DV535219
EST:     CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAG                         AGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
genomic: CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
EST: gi|211056018|gb|FL461757.1|FL461757
EST:     CTCTGGAAGGAGATGGGCTGGCAGAACTCTGATCCATCCACAGATTTTAG                         AGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
genomic: CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
EST: gi|78027658|gb|DV496045.1|DV496045
EST:     CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAG                         AGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
genomic: CTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
EST: gi|31664066|gb|CD573246.1|CD573246
EST:     TCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAG                         AGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA
genomic: TCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTA

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), 49 (downstream exon)
Score: 63

TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTACCCA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 48

TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTACCCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 47

TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTACCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttct ... atgcttgcagAGCAGCTGGGTTCATGTCCTTGGAGAATCTAATATATTTTGCCAGAAATTACCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGAAGTTGGCTTACCCTAACAGACAACTTCCTCCTCTGAAGTCAGATCTCTGGAAGGAGATGGGCTGGCAGAACTCCGATCCATCCACAGATTTTAGgttcagttctgcagtgatgacgtttcttgataaattgtcatgcattatgttgacatgatttgagccggatgatttgtattttaaagtatcctatgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG