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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttcgatgtgttatagatttttttgacagatcttaacacacataaacttttcttctcggcttagtatttcactgtttgacttccatcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAG

Basic information

species Zea mays
transcript GRMZM2G060977_T05
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060977_T05 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 10
gtaagtcttcgatgtgttatagatttttttgacagatcttaacacacataaacttttcttctcggcttagtatttcactgtttgacttccatcaatcagGAGGG---TATTATGGACCCTCTCAAGCAGTGGGCAA---GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAG
||||||||||    || ||   |  |     |||| | || ||||| |  ||||||  |    || | | | |||  || |||||||| |||  |  ||||||    || |||||| |||| |||| | |||||||    |||||||||||||| || ||||||||||| |||||||| || || |||||||| |||||      
gtaagtcttc----tgctacgaagatc----acaggt-ttgacacaaagcaactttgttaactggttaaatgtttt-ctatttgacttacattgactagGAGGAGGATACTATGGATCCTCCCAAGGAATGGGCAACAAAAAGATATTTGTTGGCAGGCTTCCACAAGAGGCAAACACGGAGGACCTAAGGCATTACTT------
















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|78107953|gb|DV526371.1|DV526371
EST:     TCCTGGATCAGCTTATGGAA                         GAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: TCCTGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|60352542|gb|DN219515.1|DN219515
EST:     AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAA                         GAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|113702665|gb|EE680169.1|EE680169
EST:     AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAA                         GAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|60342166|gb|DN209139.1|DN209139
EST:     TGGATCAGCTTATGGAA                         GAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: TGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|32837415|gb|CD977093.1|CD977093
EST:     AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAA                         GAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|148942651|gb|EC887670.2|EC887670
EST:     AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAA                         GAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|211424816|gb|FL445164.1|FL445164
EST:     AACTCT-GGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAA                         GAGGGTATTATGGGCCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|211138006|gb|FL213711.1|FL213711
EST:     AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAA                         GAGGGTATTATGGGCCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|32864876|gb|CF004558.1|CF004558
EST:     AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAA                         GAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTCTGGGTGCACCAACGCTGTATGACCATCCTGGATCAGCTTATGGAAgtaagtcttc ... catcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacataaacttttcttctcggcttagtatttcactgtttgacttccatcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAG
                                   gtttgac  putative branch site (score: 4)
                                         cttccatc  CT-rich tract
                      ttagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttcgatgtgttatagatttttttgacagatcttaacacacataaacttttcttctcggcttagtatttcactgtttgacttccatcaatcagGAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG