Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatgaaatatgaattgtcaaatcacatctaattctcaatattggtcgatgctttctttttgacatctgacctgtgcatattcttccactttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG

Basic information

species Zea mays
transcript GRMZM2G141903_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 3'ss of exon 4
tttatgaaatatgaattgtcaa-atcacat-ctaattctcaatattggtcgatgctttctttttgacatctgacctgtgcatat--tcttccactttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG
    || ||||     ||  |  ||  | | ||||| |   |  |   |      |||   ||||  | ||||  || ||||||  | |  |  |||  ||||||||||||||||| ||||| || ||||||||||| ||||| |||||||||||||| ||||||||||| |||||||||||||||||||| |||
----tggaatagatcatgcaattattgcttactaatgcgtcaattctttgctcatttttgctttggtacctgagttgagcatatggtttctcgtttttattcagGTATTTCAAGGGGCCTGAGCTTCTTGTTGATTTGCAAGATTATGATTATTCTTTGGACATGTGGAGCCTTGGTTGCATGTTTGCTGGGATG

upper sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 4
---tttatga-aatatgaattgtcaaatcacatctaattctcaatattggtcgatgctttctttttgacatctgacctgtgcatattcttccactttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG
   | ||| |  || | || |      || |      |  |||    |    |      |  ||||  |   |    ||    | |   | |    ||  | ||||| || ||||| || ||  | ||||| ||| | |||||||| ||||||||||| |||||||||||| | || ||||||||||||||||||
ggttctattatgattttaagtacttgttccctcagtgtcgtcacgtctttcagggatgctagtttttgctcatatattgca-gtgtctcttcg---tgtattagGTACTTTAAGGGCCCAGAGTTACTTGTCGATCTTCAAGACTACGATTATTCTTTGGACATGTGGAGTTTAGGATGCATGTTTGCTGGAATG

upper sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 5
tttatgaaatatgaattgtcaaatcacatctaattctcaatattggtcgatgctttctttttgacatctgacctgtg-catattcttccactttggtt--cagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG
       | |   | || |  |||   ||  | ||  |    ||  ||  |  | | |||   | ||  ||    |  ||| |||      |||||    |||||| |||||||| ||||| || || |||||| | ||||| |||||||| ||| | |||||||||||  | || ||||||||||| || |||
---gaacagtcacagttctataatgtaatgaactttactgattttatcttttgtatgtttagtagatacgatgcatctcatcttcacagtttttgggaaacagGTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG

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|149097662|gb|EE183562.2|EE183562
EST:     GCTGAGTTCTACCCTCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTA
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTA
EST: gi|60400467|gb|DN233274.1|DN233274
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
EST: gi|5895649|gb|AW036895.1|AW036895
EST:     GTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
EST: gi|149107621|gb|EE189503.2|EE189503
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTC
EST: gi|18964894|gb|BM661271.1|BM661271
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
EST: gi|31354720|gb|CD439077.1|CD439077
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
EST: gi|8366916|gb|BE049924.1|BE049924
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
EST: gi|60344732|gb|DN211705.1|DN211705
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
EST: gi|5296240|gb|AI782920.1|AI782920
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
EST: gi|19351815|gb|BM896347.1|BM896347
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
EST: gi|76925599|gb|DV170500.1|DV170500
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTTCA-GGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATT
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTT-CAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATT
EST: gi|32849417|gb|CD989098.1|CD989098
EST:     GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAG                         GTATTTCAAGGGGCCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC
genomic: GCTGAGTTCTACCATCCAGGCAAGGAATACAATGTCCGTGTTGCATCGAGgtaggttgag ... tttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgatgctttctttttgacatctgacctgtgcatattcttccactttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG
                    atctgac  putative branch site (score: 3)
                                  tattcttccacttt  putative PPT
        tttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatgaaatatgaattgtcaaatcacatctaattctcaatattggtcgatgctttctttttgacatctgacctgtgcatattcttccactttggttcagGTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA