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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataccatttctttctgtttgtttgtgctacaattatgataaacttaggtttacaagaagacagcaaatcaaaacatctgtgatattcttctcaagtgtgcttgtatgtgatagtattctctttcttgccccctcttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG

Basic information

species Zea mays
transcript GRMZM2G180704_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgataccatttctttctgtttgtttgtgctacaattatgataaacttaggtttacaagaagacagcaaatcaaaacatctgtgatattcttctcaagtgtgcttgtatgtgatagtattctctttcttgccccctcttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG
                                               |   ||||    |    | |||     ||| |       |  | |   |  |    || ||| ||| |||      ||   | |      |||||  |||| ||||| || || ||||| |||||| ||||||||||||| ||  | || || ||||| |||||| | || ||||| || ||||||||||| |||||||
--------------------------------------------gtatgtttttattttattttatcaacatgtaactttccaagcaaccattcgattttatattatatttgagagttaagaattagctacttggctttgatgtagATAATATCAGGAGTGGAATACTGCCATCGAAACATGGTGGTTCACAGAGACCTCAAGCCTGAAAACTTGCTTTTGGACTCTAAATGCAATGTAAAGATTG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ35371 (Selaginella moellendorffii), 3'ss of exon 2
gtgataccatttctttctgtttgtttgtgctacaattatgataaacttaggtttacaagaagacagcaaatcaaaacatctgtgatattcttctcaagtgtgcttgtatgtgatagtattctctttcttgccccctcttgatac-agATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG
                                                                                             ||  |     | |  ||    || |  ||   | |  | | | |     || |||| || || || || |||||||| || ||||| |||||||| ||||||||||| ||||||||||| ||  |  | || || |  |||||||| |||||||
-------------------------------------------------------------------------------------------gttcgtgctccttcgcctggtgaagaaaactgaatataactcgcacacatcaccagATCATTTCTGGAGTGGAATATTGTCACAGAAATATGGTGGTTCATCGTGATCTGAAGCCAGAAAATCTGTTGCTTGACTCTAGGTGCAATGTGAAGATTG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ17922 (Selaginella moellendorffii), 3'ss of exon 2
gtgataccatttctttctgtttgtttgtgctacaattatgataaacttaggtttacaagaagacagcaaatcaaaacatctgtgatattcttctcaagtgtgcttgtatgtgatagtattctctttcttgcccc-ctcttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG
                                                     ||| |||| | |     ||      |   ||  |||        ||||| || |   |  |  | ||  | | || | |   ||  || || ||||||| || |||||||| || || |||||||||||||| || |||||||| || ||||| || ||  | ||  | |  || ||||||| ||| ||||| |
----------------------------------------------------gtacgagaaaaaaatgtctcgtttttttcttggcattgagt----gtgtgtttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCGGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATCG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 2
gtgataccatttctttctgtttgtttgtgctacaattatgataaacttaggtttacaagaagacagcaaatcaaaacatctgtgatattcttctcaagtgtgcttgtatgtgatagtattctctttcttgcccc-ctcttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG
                                                     ||| |||| | |     ||      | | |  | | | |     ||||| || |   |  |  | ||  | | || | |   ||  || || ||||||| || |||||||| || || |||||||||||||| || |||||||| || |||||||| ||  | ||  | |  || ||||||| ||| ||||| |
----------------------------------------------------gtacgagaaaaaaatgtctcgt----ttttttctttgcattgagtgtgtgtttatggatcgtgtttttgacatgctagtcttgctggtggtatagATTATCTCGGGTGTTGAGTACTGTCATAGAAACATGGTCGTTCATCGTGACCTCAAGCCAGAGAATTTGCTTCTCGGCTCCAAATGCAGTGTCAAGATAG

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|71768950|gb|DR966887.1|DR966887
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
EST: gi|211439527|gb|FL064919.1|FL064919
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
EST: gi|148969836|gb|EE020728.2|EE020728
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
EST: gi|149088708|gb|EE177828.2|EE177828
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
EST: gi|149088317|gb|EE177414.2|EE177414
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
EST: gi|94473981|gb|EB702939.1|EB702939
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
EST: gi|211006231|gb|FL064937.1|FL064937
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
EST: gi|148974739|gb|EE025550.2|EE025550
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
EST: gi|211324790|gb|FL345978.1|FL345978
EST:     TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAG                         ATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT
genomic: TTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGAT

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: 418

TTATGTTGTTATGGAGTATGTTAAGTGTGGGGAATTATTTGATTACATTGTTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 140

TTATGTTGTTATGGAGTATGTTAAGTGTGGGGAATTATTTGATTACATTGTTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 126

TTATGTTGTTATGGAGTATGTTAAGTGTGGGGAATTATTTGATTACATTGTTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 386

TTATGTTGTTATGGAGTATGTTAAGTGTGGGGAATTATTTGATTACATTGTTGAGAAAGGTAGGCTGCAGGAGGAAGAGGCTCGCCGTTTCTTCCAACAGgtgataccat ... cttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcaagtgtgcttgtatgtgatagtattctctttcttgccccctcttgatacagATTATATCCGGTGTTGAATATTGCCATAGAAACATGGTGGTGCATCGTGATCTAAAGCCAGAAAACCTCCTATTGGATTCAAAATGCAATGTTAAGATTG
                                            tcttgat  putative branch site (score: 386)
                         tattctctttcttgcc  CT-rich tract
                     atagtatt  TA-rich tract