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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatttgtttgccatttttcggttcatgttagtttaatctattttattggacacatcacattggtcatattgtcaatgttttaacttccctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGGTAAATTGTGAAATTTGCAAACCTT

Basic information

species Zea mays
transcript GRMZM2G094255_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094255_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 4
tatatttgtttgccatttttcggttcatgttagtttaatctattttattggacacatcacattggtcatattg-----tcaatgtttta--acttccctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGGTAAATTGTGAAATTTGCAAACCTT
 |  ||| ||||  | |     |   || |   | |   | | || ||  | ||    | |||| | || |       || ||  ||||  | | |||  |||| ||||||| |||||||| |||||||| || || ||||||  |||||| ||| | |||||||||||||| ||||| |||                         
-aattttttttgttagt-----gcggatatccatgtctaccacttcatcagtcaggcta-attgataatgtgacttactctattatttactattcccccatatctagGATCTATCTGGTCGTCCTCATTTGAGTTGCGGCTTAAGTATTCCGACTGAGAGAGTTGGCACATACGATACTCAG-------------------------
















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|76281018|gb|DV020586.1|DV020586
EST:     TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG                         GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
genomic: TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTGgtaagtcaca ... ctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
EST: gi|211006666|gb|FL081503.1|FL081503
EST:     TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG                         AATCTGTCTGGTCGCCCTC
genomic: TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTGgtaagtcaca ... ctgtatccagGATCTGTCTGGTCGCCCTC
EST: gi|211003886|gb|FL081493.1|FL081493
EST:     TTGGTCATTTTACAGCACCGCTTGATGAAGCAGCGGGTGAGGTTATACTG                         GATCTGTCTGGGTCGCC-TCATTTAAGCTGTGGCTT
genomic: TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTGgtaagtcaca ... ctgtatccagGATCTGTCTGG-TCGCCCTCATTTAAGCTGTGGCTT
EST: gi|149110134|gb|EE293952.2|EE293952
EST:     TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG                         GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
genomic: TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTGgtaagtcaca ... ctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
EST: gi|88757021|gb|DY541162.1|DY541162
EST:     TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG                         GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
genomic: TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTGgtaagtcaca ... ctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
EST: gi|101397352|gb|EB820599.1|EB820599
EST:     TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG                         GATCTGTCTGGTCGCCCTCATTT
genomic: TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTGgtaagtcaca ... ctgtatccagGATCTGTCTGGTCGCCCTCATTT
EST: gi|50325237|gb|CO520363.1|CO520363
EST:     TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG                         GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
genomic: TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTGgtaagtcaca ... ctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
EST: gi|50323498|gb|CO518624.1|CO518624
EST:     TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTG                         GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA
genomic: TTGGTCATTTTACAGCACCGCTTGATGAGGCAGCGGTTGAGGTTATACTGgtaagtcaca ... ctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattggacacatcacattggtcatattgtcaatgttttaacttccctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGGTAAATTGTGAAATTTGCAAACCTT
                                  ttttaac  putative branch site (score: 2)
                                        cttccctgt  CT-rich tract
                              aatgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatttgtttgccatttttcggttcatgttagtttaatctattttattggacacatcacattggtcatattgtcaatgttttaacttccctgtatccagGATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGGTAAATTGTGAAATTTGCAAACCTT

- - - tgtttgc
- - - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - -ggacaca