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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcgtgtgatttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA

Basic information

species Zea mays
transcript GRMZM2G382104_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g58750.2 (Oryza sativa), 3'ss of exon 5
gtgagtatcgtgtgatttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
||||||||| | |   ||||||||  ||| |||||| | ||| ||| |||||||    |||| ||| || ||   |||||||||||||||||| ||||| ||||| || |||||||||||||| || ||||| ||||| |||||||||||| |||| ||||| |||||||| |||||||
gtgagtatcatatagattgtttttgtaacgtgatcatctgtgtgttttgtaacatttctatgttgtttacatggcacagGACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGATGGTAAAAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G07850.2 (Glycine max), 3'ss of exon 5
gtgagtatcgtgtg-atttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
|| ||| |  |||| ||    |||||  |||||  |  || |   |    ||| | |   ||| |||    ||  | |||||  |||| ||||| |||||  |||| ||||| ||||| || ||| ||||||| |||||||| || || |||||||||||||| |||||||| ||  | |
gtaagt-ttttgtgtatcccctttttatacatgtcc--caataattagattaata-aaaaatg-tgttagaattttgcagGATGGTAATCCTAGGCTTTCAAGTTTTGGTCTTATGAAAAATAGCAGGGATGGGAAAAGTTATAGCACAAATTTGGCATTTACCCCTCCAGAGTATCTTA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G01300.2 (Glycine max), 3'ss of exon 5
gtgagtatcgtgtg-atttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
|| ||| |  |||| ||    |||||  |||||  |  |  |   |    ||| | |   ||| |||    ||  | |||||  |||| ||||| |||||  |||| ||||| ||||| || ||| ||||||| |||||||| || || |||||||||||||| |||||||| ||  | |
gtaagt-ttttgtgtatcccctttttatacatgtcc--ctataattagattaataaaaaaatg-tgttagaattttgcagGATGGTAATCCTAGGCTTTCGAGTTTTGGTCTTATGAAAAATAGCAGGGATGGGAAAAGTTATAGCACAAATTTGGCATTTACCCCTCCAGAGTATCTCA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
-----------------gtgagtatcgtgtgatt-tgttttttcaacatgatcagca---gtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                 |  | |    |    ||  || || | | | | |  || |   || |  | |         || | |   |  | |  | |||||||  || ||||||||||| || |||||||| ||||| || ||  ||||||| | |||||||||||| |||||||| ||||| || || |||||  |||
tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G01730.2 (Glycine max), 3'ss of exon 5
------------------gtgagtatcgtgtgatt-tgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatacta--cagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                  |  | |    |    |  || ||| | | | | |  || |   |   ||||        | |  |  ||   || ||  ||||| |  || ||||||||||| || |||||||| ||||| || ||  | ||||| |||||||||||||| ||||||||||| || || || |||||  |||
ggcactgatactgtggaagaaactgctataaattagtgctttcttagcctaaatagtatgtgtgactgtcctttttctttttttcctccttattattcagGAATACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGATGGGAAAAGTTACAGTACAAATTTGGCATTCACTCCACCTGAATATCTGA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------gtgagtatcgtgtgatttgttttttcaacatgatcagcagtgggttctgtaacacagttatg-ctgtctatatacta-cagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                       ||    |  || | |||   |   |  | |     ||       | ||    | |||||  | |||  |   || |||||  |  ||||  | || |||||||| || ||||||||||||||| | ||||| ||||| ||||| |||||| |||| |  || ||||| || ||| | |
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggt-tagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S122_66V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------------gtgagtatcgtg-tgatttgttttttc--aacatga---tcagcagtgggt--------tctgta----acacagttatgctgtct---atatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                                                                                                    | ||   |  | | || ||||| |  || || |   |    ||| |          ||||||    | | | | ||| | ||       |    |||||  |  | ||  | || || ||||| || |||||||||||||| || ||||||||||| || ||||||||| |||| |  || || || |||||| | |
gtattgctcttctctgtagcagttttgaactaaaacttggtatgtcccttcccgttcctatcaagtctcgacaatcctgctatacagaacacccacatcaaatacgctaatcacttttttttacggaaaataaggttttaaagtagacctatctaatctgtagattataaattgatggtctcccacgcctttgtcagGAAGGAGATCCGCGCCTCTCTTGTTTTGGCCTCATGAAGAACAGTCGCGATGGAAAAAGCTATAGTACCAATCTGGCCTACACTCCCCCTGAATACTTAA

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------gtgagtatcgtgtgatttgttt-tttcaac-atgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                       |||      |  |  ||   |||||||     | |  ||   | || |||    |   || || |    ||  |  ||||| |  ||||  | || |||||||| || ||||||||||||||| | ||||||||||| ||||| ||||||||||| |  || ||||| || ||| |||
tcgtgtgggtttcctttggaaatagttctacttagtacgtggatttcaactgcagttaatagaatgctcagtatattaacgattctctacg-attttgtagGACGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGAAAAAGCTACAGCACCAATTTGGCTTACACTCCTCCTGAGTACTTGA

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|211173516|gb|FK981111.1|FK981111
EST:     GCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGAT                         GACTGTAACCCTAGACTTTCCTGTTTCGGCCTCATGAAGAACAGTCGGGAT
genomic: GCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcg ... tatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGAT
EST: gi|211173514|gb|FK981109.1|FK981109
EST:     GCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGAT                         GACTGTAACCCTAGACTTTCCTGTTTCGGCCTCATGAAGAACAGTCGGGAT
genomic: GCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcg ... tatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGAT

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: 233

AAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcg ... tatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

AAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcg ... tatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 179

AAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcg ... tatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

AAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcg ... tatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA
                      ctgtaac  putative branch site (score: 212)
                                           tatatacta  TA-rich tract