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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctgcagtgcttgttgaattttcaattttctatctaaatctagctgctgaagtcaatgctcatgttttgtcaaagagcatgtcttaaataaggacagaaacacattactgcatcctgtgttggcccctgttttaattttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG

Basic information

species Zea mays
transcript GRMZM2G113726_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113726_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 6
-----------------------------------gta-agcctgcagtgcttgttgaat-tttcaattttctatctaaatctagctgctgaagtcaatgctca-tgttttgtcaaaga-----gcatgtcttaaataaggacaga--aacacattactgcatcctgtgttggcccctgttttaattttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG
                                    || | | ||   |  || ||| ||  | | |  | |||    | ||       | |||||| | || | || ||||  |||||     ||||  | | |  || || ||   ||    ||| || ||    | ||| ||| ||||||| |    ||||||| ||||| |||||||| ||||||||||||| ||||||||| |||||||  ||||| |||||| |  | ||  ||||||||||||| 
gtaagcctttacttcattcatcaaactgtttatatctatatcttgttttatttattggatactcccaagtcctaatctattcgccacattcaagtcactactgaatgctttgctaaagattcttgcattccatgaggaaagaaagcctaatgttttattg-atttaatcttgccccttgtttta-taccatgcagCACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAA
















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|56461997|gb|CK986295.1|CK986295
EST:     TGGAAAAATTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAAT                         CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
genomic: TGGAAAAGTTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAATgtaagcctgc ... ttttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
EST: gi|47961405|gb|CN844114.1|CN844114
EST:     TGGAAAAATTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAAT                         CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
genomic: TGGAAAAGTTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAATgtaagcctgc ... ttttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
EST: gi|44681734|gb|CK786782.1|CK786782
EST:     TGGAAAAATTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAAT                         CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
genomic: TGGAAAAGTTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAATgtaagcctgc ... ttttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
EST: gi|44682058|gb|CK787106.1|CK787106
EST:     TGGAAAAATTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAAT                         CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
genomic: TGGAAAAGTTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAATgtaagcctgc ... ttttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
EST: gi|47962732|gb|CN845441.1|CN845441
EST:     TGGAAAAATTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAAT                         CATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT
genomic: TGGAAAAGTTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAATgtaagcctgc ... ttttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggacagaaacacattactgcatcctgtgttggcccctgttttaattttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG
                                       ttttaat  putative branch site (score: 3)
                                             ttttctgc  CT-rich tract
                                     tgttttaattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctgcagtgcttgttgaattttcaattttctatctaaatctagctgctgaagtcaatgctcatgttttgtcaaagagcatgtcttaaataaggacagaaacacattactgcatcctgtgttggcccctgttttaattttctgcagCATACATCGTTGAGCCCAGATGGTAAACTTGCTGCTATTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA