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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG

Basic information

species Zea mays
transcript GRMZM2G075485_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactg-gtccaacaggcttgttttaatttctatattggcattgttcccttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG
          ||  ||  ||  |    |||   ||| | ||   | ||| | ||| ||  | || ||      |     | | ||  |||||||| ||    | || ||||| ||| ||||||||| ||  |||||||||||||||| |||||||||||||| || ||||| || ||||||||||| ||||| |||| |||||
---------gtggcttacaaaat----ttagtgttgattaattttctatacagaaggcaatgaattgcaagtgaataattgggttccatttctattttaatttggtgcccttgtatgcagGCTTTTTTGTTCAATGATTTGCTCAGATCCAAAGCTTGATTCCCATCGCTTTAAAGATATAATTGATGAGGCAATTGCTGAAG

upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG
                                                   | ||| |  |    ||    |  |   ||  ||  ||    |  ||    ||| |     || | |||||| |||||  ||||| |||| ||||| || || ||||| |||||||| ||||||||||| ||||| ||||  || | ||  |
--------------------------------------------------gtaaaaacattgtgatgaggaagaaccttttattggatacagaatttcagtttgatattccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG
                                       ||  | | |||||      |  | | || |      |   ||  || |||| |||||      | ||  ||||   ||||||| |||||| ||||| ||||||| || || ||||||||||| ||||| ||||| || ||  |||| ||||| ||||  | ||
-------------------------------------gtaattcatcatcctttcttttcgatattgtt---gaggttgtgagttgatttatatat-----atattttcttc---ccagGCTATTCTGCTCAATGCTTTGCTCGGACCCCAAGCTTGATTCACACCGTTTCAAAGACATGCTTGATGAGGCCATTGCAGCAG

upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaac--aggcttgttttaatttctatattggcattgttcccttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG
                              |  ||  |||  || || |  | |    ||| || |     |    | | |||| | ||  |   |||||| | | |  |  | |   ||||||||||||| ||||| |||||||  | || ||||||||||| ||||| ||||| ||||| || || ||||| ||||  |  |
-----------------------------gtaattaatcatccccttgttttcattattgtcaagtttgtgagttgaagtttgtataaacat---tattggtactatatctcttt---cagGCTTTTCTGCTCAATGCTTTGCTCGAACCCCAAGCTTGATTCGCACCGTTTCAAAGATATTATCGATGAGGCCATTGCAGCGG

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|78117499|gb|DV535886.1|DV535886
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
EST: gi|78116316|gb|DV534703.1|DV534703
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTG
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTG
EST: gi|211342376|gb|FL103369.1|FL103369
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTT-CTGCGCAATG
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATG
EST: gi|71443603|gb|DR824653.1|DR824653
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
EST: gi|211339995|gb|FL103365.1|FL103365
EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCCACATGAACAG                         GCTTTTCTGCGCAATGATTTG
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTG
EST: gi|91870824|gb|EB401103.1|EB401103
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
EST: gi|211339988|gb|FL103358.1|FL103358
EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAA
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAA
EST: gi|32909541|gb|CF014353.1|CF014353
EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
EST: gi|71443604|gb|DR824654.1|DR824654
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
EST: gi|60341956|gb|DN208929.1|DN208929
EST:     AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTT
EST: gi|211339992|gb|FL103362.1|FL103362
EST:     AAAACGGACTTGAAGGAACTCTATACAAAATATAAGGGCAACATGAACAG                         GCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCAC
genomic: AAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACAGgtgatttctt ... ttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtccaacaggcttgttttaatttctatattggcattgttcccttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG
                 ttttaat  putative branch site (score: 3)
                                     ttgttcccttctatcc  putative PPT
              ttgttttaatttctat  TA-rich tract