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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggtccttctttggacccaatccttcttgcctaaattagttcccatccatcagttaactatgactgtgctaagtatcggtactggttggttataagctgttacatactttacataatagcatcacgtggattccccattcgatatgcaacagcgacagttcctctgctcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTCATCGATCCGAGGCTGGAGACCGACTACGACGCGCACGACATGGCGCGGC

Basic information

species Zea mays
transcript GRMZM2G470499_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470499_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g54700.1 (Oryza sativa), 3'ss of exon 6
gtgagtggtccttctttggacccaatccttcttgcctaaattagttcccatccatcagttaactatgactgtgctaagtatcggtactggttggttataagctgttacatactttacataatagcatcacgtggattccccattcgatatgcaacagcgacagttcctctgc-tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTCATCGATCCGAGGCTGGAGACCGACTACGACGCGCACGACATGGCGCGGC
                                                                                            |    |  |||      |  |  ||  || |     |  |  |||  |||  ||    |  | ||      |  || ||  |   |||||||| || ||  |||||   ||||||||||||||||| |||| ||| || ||  | || ||||||||||||| | ||||||||||| ||||||||| |||||
--------------------------------------------------------------------------------------------gtgagtgggcttccgagtcttgaaccgaacacgtagatttccatttgcca--cggccggtgaaagtagtcatctctgtgtgtgtccaacagGCGAGACCCCTGCTGGTGAGAGCTGTGGAGGAGGAGAACTTCGAGGAGCTGGTTGACCCGAGGCTGGAGAACAACTACGACGCGTACGACATGGGGCGGC
















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|101381709|gb|EB812912.1|EB812912
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|148995866|gb|EE035102.2|EE035102
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|71436076|gb|DR817126.1|DR817126
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|149104235|gb|EE289671.2|EE289671
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|89249349|gb|DY621135.1|DY621135
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|94477995|gb|EB706953.1|EB706953
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|88750189|gb|DY534330.1|DY534330
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|37422946|gb|CF649190.1|CF649190
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|71771807|gb|DR969744.1|DR969744
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|76914139|gb|DV165421.1|DV165421
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|110215668|gb|EC897566.1|EC897566
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|148952461|gb|EC898287.2|EC898287
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|71316884|gb|DR795129.1|DR795129
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|148963688|gb|EE014752.2|EE014752
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|148987250|gb|EE031085.2|EE031085
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|94474665|gb|EB703623.1|EB703623
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|78087049|gb|DV515442.1|DV515442
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|71763339|gb|DR961276.1|DR961276
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|101384403|gb|EB814246.1|EB814246
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|50334733|gb|CO529859.1|CO529859
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|148987251|gb|EE031086.2|EE031086
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGANCA-GAGCTGTGGAGGAGGAAAA
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGA-CAAGAGCTGTGGAGGAGGAAAA
EST: gi|148959211|gb|EC905317.2|EC905317
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|78124341|gb|DV542725.1|DV542725
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
EST: gi|71423642|gb|DR806109.1|DR806109
EST:     AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGG                         GCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC
genomic: AACCAATCATGGCATCTTCAGAGTTTCAGTCTGTGGCATTGGTTTCTTGGgtgagtggtc ... tcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgtggattccccattcgatatgcaacagcgacagttcctctgctcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTCATCGATCCGAGGCTGGAGACCGACTACGACGCGCACGACATGGCGCGGC
                                    ttcctctgctcctc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtggtccttctttggacccaatccttcttgcctaaattagttcccatccatcagttaactatgactgtgctaagtatcggtactggttggttataagctgttacatactttacataatagcatcacgtggattccccattcgatatgcaacagcgacagttcctctgctcctcaacagGCTAGGCCATTGCTGACAAGAGCTGTGGAGGAGGAAAACTACGACGACCTCATCGATCCGAGGCTGGAGACCGACTACGACGCGCACGACATGGCGCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA