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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgtttataaatcattactgtcatagagttatgcaaacaaacttatgtgatgaatcctaacacgacctttgatcctatatctacag

Basic information

species Zea mays
transcript GRMZM2G005036_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 7
ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgta-------tggctgtttataaatcattac---tgtcatagagtta-tgcaaacaaacttatgtgatgaatcctaacacgacctttgatcctatatctacag
 |||||||||| |||||||||||||||||  | ||||| ||||| || |||||||||||| | |||||||       ||  | | | | || |||||    | ||| ||  | | |    | | || |  || | |  || |||||  | || |||| || || | ||||
GTGCTCATGGGTGGAGGAGGGTCCTTCTCGACCGGTGGCCCTGGGAAAGGAATGCATTCTTGGTTGTgtaagcttaatgcttctcttttaaccattatgcatatcagagcatcaataagcatataccttggtaaagtgtcttaacatcagctgtgattctgtaccgacag

upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA13G43000.1 (Glycine max), 5'ss of exon 8
ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgtttataaatcat-tactgtcatagagtt-atgcaaacaaacttatgtgatgaatcctaacacgacctttgatcctatatctacag----------
||||| ||||||||||| ||||| ||||||||||| ||||||||||| || ||||||||  |  ||||||  | | |   || ||| | | ||    || || | ||     | ||  | | ||||  | | |  | |    | |  |  ||| | || |           
ATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGTgta-agttttacctatatcttcttctactttacagctgattttggccaa--tgtttgatttacctttgc-cattatatatttgtatttataaacttttcccatt

upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv11s0016g02870.t01 (Vitis vinifera), 5'ss of exon 7
ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgtt---tataaatcattactgtcatagagttatgcaaac----aaacttatgtgatgaatcctaacacgacctttgatcctatatctacag---
||||| ||||||||||| || || |||||||||||||| |||||||| || ||| | || ||| | |||| |  | |    || | |    | |  ||| ||  ||| |   |     | |   |||  |   ||  |  ||      |  || |  ||| | ||    
ATGCTAATGGGAGGAGGTGGATCTTTCTCTGCTGGTGGTCCTGGAAAAGGGATGTACTCACGACTATgtaagtttctcagatacacacgtgtgcattcagagttttaagttgaggttgagatacatgcaacacattttg-catacttgtgcattcagtat-tgcatatg

upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S74_253V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgtttataaatcattactgtcatagagttatgcaaacaaact-tatgtgatgaatcctaa-cacgacctttg--atcctatatctacag-------------
                           |||  | |||||||||||||| |||||||| ||||| ||||||||||||||| ||||||||||||  |  |  ||  | | || ||       ||    |  || ||||    | | |  |||   | ||   ||     || |      | | | ||                
TTCATATGCAGTGACTGTCCTACAGCAGCTTCTTGGAGGAGGAGGGTCTTTCTCTGCGGGTGGTCCTGGAAAGGGAATGTATTCTCGATTGTACACTGGGgta-agatattatccggagtatcttatcgtgaaaactctttctttaagatagtttctggtcattgatttcgtagaagtctgtttatgtttcgggtaatcaa

upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S219_95V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgtttataaatcattac--tgtcatagagttatgcaaacaaacttatg--tgatgaatcctaacacgacctttgatcctatatctacag-------------------------------------------------------------------------------------
                            ||  | |||||||||| ||| |||||||||||||| |||||||||||||||   |||||| |||  | |   |  ||  |  ||  ||  ||| |     || | | |  | | |      | || | |  | | | |   |   |    ||   ||| |                                                                                     
TTCGTGTGCTGTGACGGTTTTGCAATCTCTTCTAGGAGGAGGAGCGTCTTTCTCTGCTGGTGGTCCTGGAAAGGGAATGTTCTCTCGACTGTACACG--CGGgtaagatccaccacattgtgaagtccttgtaccattatattggaagctaataattgatgagagggtataatagggcatgattacggcatctacataagccttcattttatgaacttgactggtttgaatgtttgccgaaggaacctcatgtgggcactttcgtcatttcag

upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S37_50V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgtttataaatcattactgtcatagagttatgcaaacaaacttatgtgatgaatcctaacacgacctttgatccta----tatctacag-------------------------------------------------------------------------------------
                         |  ||| | |||||||| ||||| || ||||||||||| ||||||||||||||| | |||||||||| ||  |  ||        |      |  | |||     |   |   | ||||||         |  |||||  | |      |     || | | |                                                                                     
TTCCTATGCTGTGACTGTCTTGCAAACACTCCTTGGAGGAGGGGGGTCTTTTTCTGCTGGTGGTCCTGGAAAGGGAATGTACTCTCGATTGTATACAGGGgtaagaccggcgcattggcaacagaagctggttcattga-ttatgtagcaggctgtt-cacgatttgtagaggcaggagcattttctgatgagtaaacttgccaatgagatttttgacctgaacatcgtatttgatttcttactttattttgatttatctgttttatttgcag

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|89761459|gb|DY689465.1|DY689465
EST:     AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT                         ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
genomic: AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
EST: gi|40333865|gb|CK367935.1|CK367935
EST:     AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT                         ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
genomic: AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
EST: gi|89758987|gb|DY687957.1|DY687957
EST:     AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT                         ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
genomic: AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
EST: gi|71438038|gb|DR819088.1|DR819088
EST:     AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT                         ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
genomic: AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
EST: gi|32863948|gb|CF003630.1|CF003630
EST:     AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT                         ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
genomic: AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
EST: gi|40336960|gb|CK371030.1|CK371030
EST:     AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT                         ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
genomic: AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
EST: gi|211246196|gb|FL443898.1|FL443898
EST:     AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT                         ATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA
genomic: AGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCA

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: 207

ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 223

ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 255

ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgt ... atatctacagATCTCCGTGTCTTGACCAACTTCCAACAGATTGAATCATTCTCTGCTTTCAATAGCGTCTATAACAATTCGGGCCTTTTTGGAATTTATGCAGTCACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGTgtatggctgtttataaatcattactgtcatagagttatgcaaacaaacttatgtgatgaatcctaacacgacctttgatcctatatctacag

- - - - - - - - - - - - - - - - TGGTGG