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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA

Basic information

species Zea mays
transcript GRMZM2G169462_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtctt-gttgcataatttatgttaagctatctgttatctactcttttttgctgttt-ttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
                                | |||    ||  ||| | |||  |  ||     |     ||||||| ||| |   | | |   |||| ||||      ||| || |      ||  |    | |||||||||   ||       |||     ||| | ||  ||||| |||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||| ||||||||||||| || || || |||||||| ||||
------------------------------gttacat--ggtcacatacctttttactcacta---gagctgtttttatttaacatgtt-tacaaatcttagttg------ttaggtcagatctcct--tgatgattcttttttgaaattaaccacttaattctacttatgttttacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgttt-ttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
|| ||   |   | |||||| |  ||||  |||   |||   ||| |   ||||        || | || ||| ||||      ||||||||  |    |||| | |   ||| ||  ||   ||  | ||  | || ||||||   ||       |||      |  ||||  |||||  ||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||| ||||||||||||| || ||||| |||||||| || |
gtaacatggtcacatctattactgtttt--tgtttttca---ctagttctgttt--------ttatttaacatgtttac-----aaaatattagt----tgttacttg--ttaggtacagacttccttgatg-attcatttttgaaattaaccatttaatgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataattt-atgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA-
                                                                            ||| |||| ||    || | |  | |  || | ||| |||||||  || ||   ||  | |   ||||  |||   ||  |   |  |  |  ||    ||||  ||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||| | || || || || |||||||| ||| ||||||| | 
--------------------------------------------------------------------------aatat-taatcaagctatcatattctttatcagagtttgatgttaa--tagctaccattcaatggatttt--tgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
                                                                             ||||  |   |  || |  |  |    || |  | || |    || | | ||   |||  | | ||  |   | |  || | ||    |  ||    ||||  || |||||||| ||||| |||||||| ||||| || || || || ||||||||||||||| | || || || || ||| |||| ||| ||||||| |
----------------------------------------------------------------------------gatcttttcgtaggttatgattataaatca-agctaatatattccttttttttgcttaccatatattagtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
                                                                       ||||| |||    ||  |||  || ||||  |      || ||| | |  |||||   || || |   |||   ||||  ||  |   |  |  |  ||    ||||  ||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||| | || || || || |||||||| ||| ||||||| |
----------------------------------------------------------------------aattttaatc----aagctatcattttctttatcagattttgatggttaa-tatctaccatttaatggattt--gtgttgctgattcttatgtaatacttgttgcagTATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCA

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
gttacgaagcttc--ctctattgcaattt-tgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaat--attcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatc--tttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
||||    |  |      | || |  | | | || | ||||||    || ||    | |   ||||  || |   |   |||   ||       ||   | | || ||   | || |  |||  ||  | |   |||||    ||| | |   | ||   ||  |  ||    ||||    |||| |||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| ||| |||| ||||| || || || || ||| |||| || |
gttagcccgtcttagtattgttactgtatatattat-catcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttc-cacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
                                                                          |||| || | |   || |    ||   |||| |   ||  |||    |   |||| | |||| |  |||  ||||  |         || |  | ||    |||| |||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||| ||| | || || || || |||||||||||| |||| || |
--------------------------------------------------------------------------tttaacttagaggttaatgcaatcagattgctt---ttcagtttttatgcatgttgtatact-tcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA

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|78107197|gb|DV525615.1|DV525615
EST:     ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAG                         TTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCCACGAAG
genomic: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
EST: gi|71439100|gb|DR820150.1|DR820150
EST:     ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAG                         TTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
EST: gi|5915469|gb|AW053110.1|AW053110
EST:     ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAG                         TTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
EST: gi|5847365|gb|AW000444.1|AW000444
EST:     ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAG                         TTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
EST: gi|24765651|gb|CA400810.1|CA400810
EST:     ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAG                         TTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
                              ggctaac  putative branch site (score: 2)
                                        tctttttttccac  putative PPT
                                 taacaaatcttttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA