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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcagccatgcctgcttttcacatgcccttgttttgagcgtaagcttcaaagggttccgaaaatgatgaactgaaaatttgtttttggggacaagcttttgaatagatcatactaggcttttccccttcggaagcttctgtcagatgtcaaacctggattttatgcataaactgcatttatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCATCATTGGAGACGACTCCTCTGTATTTGTGGAGACCGATCGCACATCATG

Basic information

species Zea mays
transcript GRMZM2G077299_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 3
gtgattcagccatgcctgcttttcacatgcccttgttttgagcgtaagcttcaaagggttccgaaaatgatgaactgaaaatttgtttttggggacaagctt--ttgaatagatcatactaggcttttccccttcggaagcttctgtcagatgtcaaacctggattttatgcataaactgcatttatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCATCATTGGAGACGACTCCTCTGTATTTGTGGAGACCGATCGCACATCATG
                                                                                          | | | || ||   | | ||  |  ||| || ||  || |     |||||||    | | ||||    | | | | | |       |     |||||||  |||| ||||||||||||||||  ||||| |||||||||||||| ||||||||||| |||||||| ||||| ||  ||||||||| ||| ||||| || |||||
-----------------------------------------------------------------------------------------ggagcataaactggatgggatgcaaaataatatgccctttcat---ggaagctatattgacatgtagggcttag-tataaccagcttatgagttttatgc-acagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGAGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG

upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 3
gtgattcagccatgcctgcttttcacatgcccttgttttgagcgtaagcttcaaagggttccgaaaatgatgaactgaaaatttgtttttggggacaagcttttgaatagatcatactaggcttttccccttcggaagcttctgtcagatgtcaaacctggattttatgcataaactgcatttatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCATCATTGGAGACGACTCCTCTGTATTTGTGGAGACCGATCGCACATCATG
                                                                                    | ||  | | | || ||     || ||  ||| || ||  ||    |   |||| |    | | || |      | | | | |   |   |     |||||||  |||| ||||||||||||||||  ||||| |||||||||||||| ||||||||||| ||||| || ||||| ||  ||||||||| ||| ||||| || |||||
------------------------------------------------------------------------------------gattaagagcataaactc---gatggaaaataatatgcccttttttt---gaagttatattgacatttagggtttag-tataaccaacttatgagttttatgc-acagGTTTTGAAGCTGGAGGCCCTCATACCCCATCAAACATTGATCCATGGTCCATAATTGGTGATGACTCTTCCATATTTGTGGCGACTGATCGAACGTCATG
















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|71769116|gb|DR967053.1|DR967053
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|211106638|gb|FL406855.1|FL406855
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|6194987|gb|AW147091.1|AW147091
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|211024644|gb|FL381981.1|FL381981
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|211518127|gb|FL378400.1|FL378400
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|71769433|gb|DR967370.1|DR967370
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|211410871|gb|FL399291.1|FL399291
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|6194981|gb|AW147085.1|AW147085
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|101399286|gb|EB821516.1|EB821516
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCCATACTCCATCAAACATTGACCCATGGTCC
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCC-ATACTCCATCAAACATTGACCCATGGTCC
EST: gi|211542545|gb|FL409073.1|FL409073
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|74232033|gb|DT639947.1|DT639947
EST:     CACCCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGG
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGG
EST: gi|211152046|gb|FL419672.1|FL419672
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTNCC
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGT-CC
EST: gi|211148949|gb|FL408684.1|FL408684
EST:     CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCMTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
EST: gi|211464409|gb|FL419840.1|FL419840
EST:     CAACCATGCAGGGGCTGGTGGCATATNGGCTGAACTTGTTAGTAACAGAG                         GGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA
genomic: CAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAGgtgattcagc ... tatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttctgtcagatgtcaaacctggattttatgcataaactgcatttatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCATCATTGGAGACGACTCCTCTGTATTTGTGGAGACCGATCGCACATCATG
                        attttatgcataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattcagccatgcctgcttttcacatgcccttgttttgagcgtaagcttcaaagggttccgaaaatgatgaactgaaaatttgtttttggggacaagcttttgaatagatcatactaggcttttccccttcggaagcttctgtcagatgtcaaacctggattttatgcataaactgcatttatgctgcagGGTTTGAAGCTGGAGGCCTCCATACTCCATCAAACATTGACCCATGGTCCATCATTGGAGACGACTCCTCTGTATTTGTGGAGACCGATCGCACATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA