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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catattggatcaatcttgttaatgtaatgtatattacattggtttctagtcaggctgattttttttggaaaggttttttgaaatgtttttctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCCTTGTGTCATGGTAAGAGGGTCATGTTGGAGCATGTTGGTGGGTTTGCTG

Basic information

species Zea mays
transcript GRMZM2G155323_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155323_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g50510.1 (Oryza sativa), 3'ss of exon 3
catattggatcaatcttgttaatgtaatgtatattacattggtttctagtcaggctgattttttttggaaaggttttttgaaatgtttttc-------tttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCCTTGTGTCATGGTAAGAGGGTCATGTTGGAGCATGTTGGTGGGTTTGCTG
        |||| | |||  | |   || | | || |||||  || | | ||  ||  |    || |||  |  | ||    || |||| |        || ||||||||||||||||||||||||| || ||||||||||||||||||||||| ||||||||||||||| | ||||||||| ||||||| ||||||||||||||||
------ttatcagtgttgcaattaatatatgtgtttcattgcattgttg-cactctagtcaggttgggatggaatgttctgtatattttacagcagctcttctacagGTGAAAATAATTGGAGTGGAGCCATCAGATGCAAATGCAATGGCATTGTCCTTGTGTCATGGTCAAAGGGTCATGCTGGAGCAAGTTGGTGGGTTTGCTG

upper sequence: GRMZM2G155323_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 3
catattggatcaatct---tgttaatgtaatgtatattacattggtttctagtcaggctgattttttttggaaaggttttttgaaatgtttttctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCCTTGTGTCATGGTAAGAGGGTCATGTTGGAGCATGTTGGTGGGTTTGCTG
  | || | | || ||   | ||| | |    ||||  | | ||         ||       |||  ||  ||    |  |   ||| | |||   ||||||||| || || ||||| ||||| ||||  |||||||||||||||||||| || ||   ||| | | |||| |||||| | || || || || || ||||| |
agtgtttggttaacctatttcttattatgtcatataggagagtgaggctggaacaccaactatttcattacaagcactaatcataatatcttt---tgtacagGTAAAGATTATTGGGGTGGAGCCCTGTGATGCAAATGCAATGGCATTGTCGTTACATCACGATCAGAGAGTCATGCTAGACCAGGTGGGAGGTTTTGCGG
















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|74234813|gb|DT642727.1|DT642727
EST:     GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAG                         GTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
genomic: GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAGgtctgctttc ... ctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
EST: gi|60338910|gb|DN205883.1|DN205883
EST:     GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAG                         GTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
genomic: GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAGgtctgctttc ... ctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
EST: gi|67017679|gb|CO446428.1|CO446428
EST:     GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAG                         GTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
genomic: GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAGgtctgctttc ... ctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
EST: gi|50324583|gb|CO519709.1|CO519709
EST:     GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAG                         GTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
genomic: GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAGgtctgctttc ... ctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
EST: gi|60354060|gb|DN221033.1|DN221033
EST:     GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAG                         GTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
genomic: GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAGgtctgctttc ... ctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCC
EST: gi|26558651|gb|CA830886.1|CA830886
EST:     TGGATTAATTGCTGGAATTGCTGCCTATGTAAAAACGGGTTCGCCCAGAG                         GTGAAAATAATTGGAGTGGAA
genomic: TGGATTAATTGCTGGAATTGCTGCCTATGTAAAA-CGGGTTCGCCCAGAGgtctgctttc ... ctttgtacagGTGAAAATAATTGGAGTGGAA
EST: gi|87156844|gb|DY401633.1|DY401633
EST:     GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAG                         GTGATAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTAT
genomic: GTGGATTAATTGCTGGAATTGCTGCCTATGTAAAACGGGTTCGCCCAGAGgtctgctttc ... ctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagtcaggctgattttttttggaaaggttttttgaaatgtttttctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCCTTGTGTCATGGTAAGAGGGTCATGTTGGAGCATGTTGGTGGGTTTGCTG
       ggctgat  putative branch site (score: 4)
                                      tgtttttcttt  putative PPT
                            ttttttgaaatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catattggatcaatcttgttaatgtaatgtatattacattggtttctagtcaggctgattttttttggaaaggttttttgaaatgtttttctttgtacagGTGAAAATAATTGGAGTGGAACCCTCAGATGCAAATGCAATGGCATTATCCTTGTGTCATGGTAAGAGGGTCATGTTGGAGCATGTTGGTGGGTTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - caggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaatg