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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgggtcttctattttgatttaatttcattgttgctggcacactttattctccatgttatgacttctcctaagatatccagctcctttcctacttggtttaagtacagttgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT

Basic information

species Zea mays
transcript GRMZM2G136803_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136803_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 3'ss of exon 17
--------------------gtaattgggtct-----tctattttgatttaatttcattgttgctggcacactttattctccatgttatgacttctcctaagatatccagctcctttcctacttggtttaagtacagtt-gttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT-----------------------------------------------------
                     ||||     ||     | | | || |  ||   | ||  ||       ||| | |   |     ||   | |      || ||||| |      |   ||        |  ||| |||  ||||||||||||| |||||||| |||||||||||||||  ||||||||| |||                                                     
gtaattcatatcgagtgcatataatccatgctacaactttctcttaacctatcctgatccttttcaatccacataaaaatattatttgaaattctcaacaaaatatc-attgaaatcattagaaataaaacatactgtttattctgcagAATATAGTCCTTATTAGAGATCCAGAGGACAGCACAAAATTTTATCCCCGCTTCAACCAGGAGGATACTTCAAGTTTTAACGATCTAGATGAACATAG
















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|32836690|gb|CD976368.1|CD976368
EST:     GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
EST: gi|32932023|gb|CF036835.1|CF036835
EST:     TTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
genomic: TTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
EST: gi|211541853|gb|FL147715.1|FL147715
EST:     GGGTAGAGAAAGAGGACAGTATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCC
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCC
EST: gi|211541851|gb|FL147713.1|FL147713
EST:     GGGTAGAGAAAGAGGACAGTATCCGACGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGG
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGG
EST: gi|32930164|gb|CF034976.1|CF034976
EST:     GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
EST: gi|211153097|gb|FL147716.1|FL147716
EST:     GGGTAGAGAAAGAGGACAGTATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGA
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGA
EST: gi|32931864|gb|CF036676.1|CF036676
EST:     TGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
genomic: TGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
EST: gi|78120827|gb|DV539211.1|DV539211
EST:     GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTTCACAAAATTCTATCC
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcctaagatatccagctcctttcctacttggtttaagtacagttgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT
                                            ttgttct  CT-rich tract
     taagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgggtcttctattttgatttaatttcattgttgctggcacactttattctccatgttatgacttctcctaagatatccagctcctttcctacttggtttaagtacagttgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA