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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttttaaacatttcatcagaaatcaaatggttactttagtcataaattgttcctgtgacctaatactggaattaagacttacagcaagttatgtgaatgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAGTGGGAGAATTTTGTCACAAGAAATCCTTCCTTGATGAAGATAATGACTC

Basic information

species Zea mays
transcript GRMZM2G107575_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107575_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g41510.1 (Oryza sativa), 3'ss of exon 6
gttcttttaaacatttcatcagaaatcaaatggttactttagtcataaattgttcctgtgacctaatactggaattaagacttacagcaagttatgtgaatgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAGTGGGAGAATTTTGTCACAAGAAATCCTTCCTTGATGAAGATAATGACTC
     |||  |||||| || | |||   ||||  || || |    ||  |  |||  ||| | ||  ||  || ||||||||||||   | |||||||  | ||| ||||| ||||||||||||||| | ||||||||||| | ||||||||||||||||||||||||||||||| |||| ||||| || ||  |||||||||||||||
----gtttggacatttgattaaaaa---aatg--tagttaaaatgtacgtaattctggtgtcttatgac-agagttaagacttacaatgacttatgtggttaatggcagACGTTTTCAGATGCTGATACTAATCAGGATGGGAGAATAGATAGAACAGAGTGGGAGAATTTTGTCTCAAGGAATCCCTCTTTATTGAAGATAATGACTC
















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|78544021|gb|DV621519.1|DV621519
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|86466680|gb|DY233050.1|DY233050
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|22542695|gb|BU093133.1|BU093133
EST:     TCCTGGATAAG                         CCATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: TCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|211255132|gb|FL091665.1|FL091665
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|91053272|gb|EB163690.1|EB163690
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGAT
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGAT
EST: gi|78085933|gb|DV514326.1|DV514326
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|60358131|gb|DN225104.1|DN225104
EST:     GATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: GATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|14203857|gb|BG837534.1|BG837534
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|16918239|gb|BM073651.1|BM073651
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGG-AAAATAGANTAGAACAGA
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGA-TAGAACAGA
EST: gi|149016909|gb|EE045638.2|EE045638
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|76018012|gb|DT945182.1|DT945182
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAG
EST: gi|71427887|gb|DR808937.1|DR808937
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|67010361|gb|CO439110.1|CO439110
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGGATGGAAAAATAGATAGAACAGA
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCA-GGATGGAAAAATAGATAGAACAGA
EST: gi|86468276|gb|DY234646.1|DY234646
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
EST: gi|78085932|gb|DV514325.1|DV514325
EST:     AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAG                         ACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG
genomic: AATCAGAAATGAGGCTATCTGATGAGATCATTGAGACAATCCTGGATAAGgttcttttaa ... atgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtgacctaatactggaattaagacttacagcaagttatgtgaatgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAGTGGGAGAATTTTGTCACAAGAAATCCTTCCTTGATGAAGATAATGACTC
                        gacttac  putative branch site (score: 2)
                  aattaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttttaaacatttcatcagaaatcaaatggttactttagtcataaattgttcctgtgacctaatactggaattaagacttacagcaagttatgtgaatgatgacagACATTTTCAGATGCTGATGCAAATCAGGATGGAAAAATAGATAGAACAGAGTGGGAGAATTTTGTCACAAGAAATCCTTCCTTGATGAAGATAATGACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA