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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaattactcatgattgattgattgatagccgcttatatgttccccatggtatcaatacgccatttggtgttgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG

Basic information

species Zea mays
transcript GRMZM2G023652_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023652_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g36340.1 (Oryza sativa), 3'ss of exon 5
gtaagaaattactcatgattgattgattgatagccgcttatatgttccccatggt---atcaatacgccatttggtgttgtgct---gcagAAGTACCAATACTCCGCGTGCAGCAGCTC---GCAAGAGTGCTGCTGTTGCTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG
     |||  | |  |  ||  ||||| | | ||   || | | | |||  || |   || || | |  |  || |  | |  |   |||| |||||||||||||| || ||||| ||||   |||||| |||||||| |||||||||||||||||||||  || ||||||||||||||||||| ||||||
---gtaaagcatttttattttcttgatagct-gctctttttttatgccctgtgtttttattaacatgaaacatgctcatttattcatgcagGAGTACCAATACTCCCCGAGCAGCTGCTCAACGCAAGAATGCTGCTGCTGCTGCTGGTTTTAGTTTCAGGCTGCAGGAGCGTGCTGAGAAGAGGAAGGAG
















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|31355088|gb|CD439445.1|CD439445
EST:     AAACAAATGCAGCCAGGGAAAACAGAGGATGATGTGCGCTCTACCACATC                         AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
genomic: AAACAAATGCAGCCAGGGAAAACAGAGGATGATGTGCGCTCTACCACATCgtaagaaatt ... tgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
EST: gi|21809702|gb|BQ668020.1|BQ668020
EST:     AAACAAATGCAGCCAGGGAAAACAGAGGATGATGTGCGCTCCACCACATC                         AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
genomic: AAACAAATGCAGCCAGGGAAAACAGAGGATGATGTGCGCTCTACCACATCgtaagaaatt ... tgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
EST: gi|21843366|gb|BQ703947.1|BQ703947
EST:     GCAGCCAGGGAAAACAGAGGATGATGTGCGCTCCACCACATC                         AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
genomic: GCAGCCAGGGAAAACAGAGGATGATGTGCGCTCTACCACATCgtaagaaatt ... tgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
EST: gi|21891697|gb|BQ744910.1|BQ744910
EST:     AAACAAATGCAGCCAGGGAAAACAGAGGATGATGTGCGCTCCACCACATC                         AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
genomic: AAACAAATGCAGCCAGGGAAAACAGAGGATGATGTGCGCTCTACCACATCgtaagaaatt ... tgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
EST: gi|31355396|gb|CD439753.1|CD439753
EST:     AAACAAATGCAGCCAGGGAAAACAGAGGATGATGTGCGCTCTACCACATC                         AAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
genomic: AAACAAATGCAGCCAGGGAAAACAGAGGATGATGTGCGCTCTACCACATCgtaagaaatt ... tgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC
EST: gi|22542624|gb|BU093062.1|BU093062
EST:     CCAGGGAAAACAGAGGATGATGTGCGCTCCACCACATC                         AAGTACCAATACTCCTCGTGCAGCAGCTCGTAAGAGTGCTGCTGTTGCTGC
genomic: CCAGGGAAAACAGAGGATGATGTGCGCTCTACCACATCgtaagaaatt ... tgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagccgcttatatgttccccatggtatcaatacgccatttggtgttgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG
       ttatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaattactcatgattgattgattgatagccgcttatatgttccccatggtatcaatacgccatttggtgttgtgctgcagAAGTACCAATACTCCGCGTGCAGCAGCTCGCAAGAGTGCTGCTGTTGCTGCTGGTTTTAGTTTCAGATTGGAGGAGCGTGCTGAGAAGAGAAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG