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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgttagtcactgccagccacttcgattgggtggagtagacaactgttggactatggttgaaccatctttcttttttttcgcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCTGTCCGCGTCGGGCAAGCGGTCGACGTGGTTGGTCAGGCAGGAAGGCCGA

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T03 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 23
gtatgtttgttagtcactgccagccacttcgattgggtggagtagacaactgtt--ggactatggttgaaccatctttcttttttttcgcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCTGTCCGCGTCGGGCAAGCGGTCGACGTGGTTGGTCAGGCAGGAAGGCCGA
||||| |   |  |   |    | || ||   |||  | | | | || ||| ||  | ||||   ||||          | | || | |  ||||||||| || |||||||| || || || |||||||| |||||||| || || || || || || |||||||| || || |||||||||||||| |||||||| |
gtatggtccatt-tagttaattgacagttttgttgc-tagtgcaaactactatttggtactaaaattgagt--------tctcttcttgtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA
















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|32929670|gb|CF034482.1|CF034482
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32926108|gb|CF030920.1|CF030920
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|32841969|gb|CD981650.1|CD981650
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|211100368|gb|FL070846.1|FL070846
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32926755|gb|CF031567.1|CF031567
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGGCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTA
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTA
EST: gi|211100372|gb|FL070850.1|FL070850
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32925375|gb|CF030187.1|CF030187
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|32867559|gb|CF007241.1|CF007241
EST:     TCCTAGGGAGATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32925086|gb|CF029898.1|CF029898
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|211100371|gb|FL070849.1|FL070849
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32925553|gb|CF030365.1|CF030365
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACCGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|60347371|gb|DN214344.1|DN214344
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|6031296|gb|AW076153.1|AW076153
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32926620|gb|CF031432.1|CF031432
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTA
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTA
EST: gi|5847123|gb|AW000202.1|AW000202
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|211100370|gb|FL070848.1|FL070848
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32849654|gb|CD989335.1|CD989335
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|32928954|gb|CF033766.1|CF033766
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|18175836|gb|BM351006.1|BM351006
EST:     ACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: ACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32841970|gb|CD981651.1|CD981651
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|32925292|gb|CF030104.1|CF030104
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCT
EST: gi|32928817|gb|CF033629.1|CF033629
EST:     TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
EST: gi|32925632|gb|CF030444.1|CF030444
EST:     TCCTAGGGAAATACCACTACATCCTCTACATCATTGTCCTGGCAATGCAG                         CCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT
genomic: TCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGT

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: 478

TGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCTGTCCGCGTCGGGCAAGCGGTCGACGTGGTTGGTCAGGCAGGAAGGCCGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 318

TGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCTGTCCGCGTCGGGCAAGCGGTCGACGTGGTTGGTCAGGCAGGAAGGCCGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 215

TGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCTGTCCGCGTCGGGCAAGCGGTCGACGTGGTTGGTCAGGCAGGAAGGCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 405

TGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTGGCAATGCAGgtatgtttgt ... gcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCTGTCCGCGTCGGGCAAGCGGTCGACGTGGTTGGTCAGGCAGGAAGGCCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagacaactgttggactatggttgaaccatctttcttttttttcgcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCTGTCCGCGTCGGGCAAGCGGTCGACGTGGTTGGTCAGGCAGGAAGGCCGA
                           ccatctttcttttttt  CT-rich tract
                             atctttctttttttt  TA-rich tract