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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattcgtttgattgttcattccacatgtttctgggataaagtagatgttttgctatggaccttagtatgcaacttgtggtttgaatatttttaga...

Basic information

species Zea mays
transcript GRMZM2G047855_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattcgtttgattgtt-cattccacatgtttctgggataaagtagatgttttgctatggaccttagtatgca-acttgtggtttgaatatttttaga
||||| |||||||| |||||||| ||||| ||||| |||||||| |||||||| ||||| |||||||||||     |||||||| |  | |  ||||| | ||  ||  |||  | ||| |||| ||||     ||  |||   | || ||       | ||||    
ATATTCCGCAAGGAGCCATTCTTCTATGGTCATGATAACCATGATCAACTTGTCAAGATCGCAAAGgtaagtcccagtttgattctggcctctcacatttctcaagggaaaaa-aaatggtttggtatgcctgataaaatgtttagttatgcaactcgtgttttgga-

upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaagg-----attcgtttgattgttcat-tccacatgtttctgggataaagtagatgttttgctatggaccttagtatgcaacttgtggtttgaatatttttaga
|| || |||||||| || || || |||||||| |||||  |||| |||||||||||||||||||||| |||       | |  | | ||| | |  | || | |  | |   |      |    ||    |||     || ||| |  || | |  ||||     || | ||
ATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAGgcaagctcattgtcctctgggttgattaccttcataagcgttttctaatctacatggattaaaatattaggttttgtacgtcacatat--tttg----cttctgga

upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 7
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgta----aggattcgtttgattgtt--cattccacatgtttctgggataaagtagatgttttg--ctatggaccttagtatgcaacttgtgg-----tttgaatatt---tttaga----------------------------
|| ||||| ||||| |||||||||||||| ||||||||  |||| || |||||||||||||| |||||        ||    || | | |   | ||| |   ||  |||       |||  | || ||     |    | |  | ||   ||   ||     ||| ||| ||   | || |                            
ATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAGgtgctcggaaatctcatttactatcagccttcaatcagtcactgctcattcgtaatttttctgaatcgtttctcctcctgtgtttctcaaggccatgtttaaatcttcgttctaaatctaatctttgttgttacctgaaatcag

upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgt-----------------aaggattcgttt------gattgt---tcattccacatgtttctgggataaagtagatgttttgctatggaccttagtatgcaacttgtggtttgaa---tatttttaga---------------
|||||||| ||||| |||||||||||||| ||||||||  |||| ||||||||||||||||| |||||                 |  |||| |  |        || |   ||| |    || | | | | |||||  ||   | || || |    |  |     ||| ||||| |||||    ||| |||                  
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaa-agtcatattactgtctttcgcaacgc-caagttgtgttttgagccttatctttgtgggtgtctgataccag

upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattcgtttgattgttcattccacatgtttctgggataaagtag--atgttttgctatggaccttagtatgcaacttgtggtttgaatatttttaga
||||||||||| |||||||||||||||||||||||||| || || || || ||||||||||| |||||    |  ||    ||   |  |||    ||||| ||   |    | |   ||||| |                                           
ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGgttttaaa-cgcagaatgtctgtttcttgctgtttttgacgttggcttgtggtgtttag-------------------------------------------

upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 6
lower sequence: EFJ28543 (Selaginella moellendorffii), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc--gtttgattgttcattccacatgtttctgggataaagtag--atgttttgctatggaccttagtatgcaacttgtggtttgaatatttttaga
||||||||||| |||||||||||||||||||||||||| || || || || ||||||||||| |||||    |  |  |  ||  ||||  || |   ||||| ||   |    | |   ||||| |                                           
ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGgttttaaacccagaatgtctgtttgttgc---tgtttttgacgttggcttgtggtgtttag-------------------------------------------

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|67025945|gb|CO454694.1|CO454694
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGA-CAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|71761092|gb|DR959029.1|DR959029
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|6095381|gb|AW120048.1|AW120048
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|149085357|gb|EE174864.2|EE174864
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|31998439|gb|CD662075.1|CD662075
EST:     ATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: ATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|149097606|gb|EE183499.2|EE183499
EST:     CATTCTTTTATGGCCATGACAACCAGGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|60345677|gb|DN212650.1|DN212650
EST:     ATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: ATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|32839753|gb|CD979434.1|CD979434
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|32925412|gb|CF030224.1|CF030224
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|7216891|gb|AW563013.1|AW563013
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|71446426|gb|DR827476.1|DR827476
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|110941068|gb|EE161225.1|EE161225
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|30705895|gb|CD058961.1|CD058961
EST:     GTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: GTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|14203981|gb|BG837658.1|BG837658
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|60340774|gb|DN207747.1|DN207747
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|30706066|gb|CD059017.1|CD059017
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|148929900|gb|EE285653.2|EE285653
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|32870873|gb|CF010555.1|CF010555
EST:     AAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: AAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|71446427|gb|DR827477.1|DR827477
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAGG                         GTC-TTGGGACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|7135281|gb|AW498007.1|AW498007
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|19436338|gb|BM952748.1|BM952748
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
EST: gi|6095382|gb|AW120049.1|AW120049
EST:     CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAG                         GTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG
genomic: CATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAG

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: 337

ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 356

ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattc ... ttattttcagGTCCTTGGAACAGATGGGTTGAATGCTTATTTGAACAAGTATCACATTGAGCTGGACCCTCAACTTGAAGCTCTTGTTGGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTTCGCAAGGAACCATTCTTTTATGGCCATGACAACCATGACCAACTTGTGAAGATTGCAAAGgtaaggattcgtttgattgttcattccacatgtttctgggataaagtagatgttttgctatggaccttagtatgcaacttgtggtttgaatatttttaga

- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG