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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT

Basic information

species Zea mays
transcript GRMZM2G069765_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 4
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT
                                                    |  ||  | | | | || |||| ||  |  ||     |     ||   |       |  || | |  |  |     ||| | | | || || ||||    |   |  |   | |||| | |  |     |  |  |||||||||||| || ||||| |||||||||||||||||||||||||||||||| ||||||||||||||| |||                              
---------------------------------------------------gtatgtggaacgttagatgttttctctctgttgagtactactgatgaaattattagtctgatgtgttaaattgccaatattttctg-ctaatgtatgaattagtactta---atctaactttcttgtcactctttggcagTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTCATTGTTTTAG------------------------------

upper sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G28650.3 (Glycine max), 3'ss of exon 5
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtaccta-attgtggttgtgttaa----tgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT
             | || ||  |||   ||    | | | |||||     | |||  ||  | | | | ||  |    | ||  |        |      |  |       | |     || |   || || |   |  |  ||| | ||    ||   |  |||| | | |||  |  | ||      | | ||||||||||| ||  ||||||| || || ||||||||||| || ||||| || |||||||||||  |||| |                              
------------gtatttgtatctt--ttgcttcactttattgatattgctgtcacacatacgttatacatactgctatatactgcactgcactccagactatgtcttgtgaaaacatcacttctgtgaatctaaggcttagtttctctttattgtgaaacttaccaacactgtcctcttattggaatgtatacagTCTATGATTGAGTTAAGTCGCACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG------------------------------

upper sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 2
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT
                                                                                         || |    ||          | ||  ||  || |  |    | |     ||| ||  ||| |||| |  |   |||     | |  ||  | |    ||||||||||||| ||| | ||||| || || |||||||||||||| ||||| || || ||||||||  |||| |                              
----------------------------------------------------------------------------------------gtgaaaccatggctttct-ttctatgcattgactttttaaggtttaattgctgtttggtgt-gcaattttctaatactgctatattatttggatgg-atgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG------------------------------

upper sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 5
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagacc-ccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtg--cagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT
||||     ||  | |   | ||||   ||     |  |  | |   |   || |  ||   |   | ||| |  | |  |    |  | || | ||| ||| || | |  ||  | | |   ||||   | |   ||| |   || | |||  |  |  |   ||    ||    || | | |||||   ||||||||||| ||| ||||||| || || || ||||||||||| ||||| || |||||||||||  |||| |                              
gtat-ttgtatcttttgcttcgctttattgatattgctttgtcacacatacattataca--tactgc-tatatactgcactgcactcca-ggctatgtcttgtgaaagcatcacttctgt---taatctaaggcttagtttctctt-tattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG------------------------------

upper sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtgcagt-ctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT
                                                                                                               |  | |  ||||   | ||| |   || ||  || |  ||    ||   |  || | | || ||  | || | || ||||||| ||||| ||  | || ||||| || |||||||||||||||||||| || || ||||| ||||||||||                              
----------------------------------------------------------------------------------------------------------gttttacttctg-acctttctctatctattgttcttgttaaaatt----gttttacttatccatttttgactctggtgat-tgcagTCAATGATTGAGTTGAGCCGTACGCAAGATGAAGAAGTTGGTGATGGGACAACGTCTGTTATTGTTCTAG------------------------------

upper sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtg-cagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT
                                                                              ||| | |    |  |||| |  ||   | |  |   | |  |  || ||        |  | | || |  ||||  |||    | ||  | | |          | |    ||||| ||||| ||| |||| || ||||| |||||||||||||||||||| ||||| || ||||||||||| |                              
---------------------------------------------------------------------------atttttttagcttttaaattttttctgttgggcttc---tgtcaatttagttcctcaaaactctgtcatcttagttgtgagttttttatatatgact----------tga----cagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG------------------------------

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|33093832|gb|CF053826.1|CF053826
EST:     ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAG                         TCTATGATCGAACTAAGTCGTAC
genomic: ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTAC
EST: gi|6021027|gb|AW065955.1|AW065955
EST:     ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAG                         TCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACT
genomic: ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACT
EST: gi|211229393|gb|FL136781.1|FL136781
EST:     ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAG                         TCTATGATCGAACTAAGTCGTACACGGGATGAAGAAAGTTGGTGATGGCAC
genomic: ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAA-GTTGGTGATGGCAC
EST: gi|211231449|gb|FL136785.1|FL136785
EST:     TGGTAATGGCATTTTGAGGGAAATAGACATTGCAC-CCCTGCTGGCCA-G                         TCTATGATCGAACTAAGTCGTACACAGGATGAAGAAAGT-GNTGATGGCA
genomic: TGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTG-CCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAA-GTTGGTGATGGCA
EST: gi|211231451|gb|FL136787.1|FL136787
EST:     ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAG                         TCTATGATCGAACTAAGTCGTACACAGGATGAANGAAAGT-GGTGATGGCA
genomic: ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAA-GAA-GTTGGTGATGGCA
EST: gi|211231448|gb|FL136784.1|FL136784
EST:     ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAG                         TCTATGATCGAACTAAGTCGTACACGGGATGAAGAAGTTGGTGATGGCACT
genomic: ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACT
EST: gi|211229392|gb|FL136780.1|FL136780
EST:     ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAG                         TCTATGATCGAACTAAGTCGTACACAGGATGAAAAAGTT
genomic: ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTT
EST: gi|32865501|gb|CF005183.1|CF005183
EST:     ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAG                         TCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACT
genomic: ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACT
EST: gi|149082543|gb|EE171738.2|EE171738
EST:     ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAG                         TCTATGATCGAACTAAGTCGTACACGGGATGAAGAAGTTGGTGATGGCACT
genomic: ATGGTAATGCCATTTTGAGGGAAATAGACATTGCACACCCTGCTGCCAAGgtatgccaaa ... taatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT
                                          tgttaat  putative branch site (score: 3)
     atttatgtt  TA-rich tract