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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatactagcaggatgcaaatccctatcttgtcatgactctgcatgcgatgtcctattgttgggatttgtttcattgctatttgggctatattgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTGTTGCTGATCCAACCTTTG

Basic information

species Zea mays
transcript GRMZM2G022876_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022876_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g34950.2 (Oryza sativa), 3'ss of exon 3
aaatactagcagg-atgcaaatccctatcttgtcatgactctgcatgcgatgtcctattgttgggatttgtttcattgctatttgggctatattgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTGTTGCTGATCCAACCTTTG
 ||| ||  | |  ||  | | |   |||   |  |   | |      | ||   | |   |    ||  |||  ||||| | ||||| || || ||||||| ||||||||||||||||||||||| |||||||| |  || || || ||||| || ||||| ||||| |
-aatcctctctgctatttagagcaggatccactggttcgtattatcatgttgatatttgtataaagttgatttacttgctttatgggcaatctttttccagGGTTGGCTATCAAAGATTTTTGGCAAGTTGATGACCAGACAATCGTGTTTGTCGCCGATCCCACCTTCG

upper sequence: GRMZM2G022876_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g01400.t01 (Vitis vinifera), 3'ss of exon 3
-----------aaatactagcaggatgcaaatccctatcttgtcatgactctgcatgcgatgtccta-----ttgttgggatttgtttcattgctatttgggctatattgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTGTTGCTGATCCAACCTTTG
             ||  |   |  ||  |  ||  ||  |  || |   | ||  ||   |    ||     |||  || |    |   ||  || |     ||  | | || |||| ||||| || ||||| |||||||| || |||||  | |||||||| |||||||||||||| |||||||
gtatattttattgatctttaaataatttatttctttacttcttcctacttttgtttgtcctagtttaaaaaattgaaggaacaactgaaatcactttaattcctcaacttttacagGGTTGGCCATTAAAGAATTTTGGCAAGTAGATGATAGAACTATTGTCTTTGTTGCTGATCCCACCTTTG
















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|16377665|gb|BI992046.1|BI992046
EST:     TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG                         GATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
genomic: TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTGgtgagttttt ... attgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
EST: gi|22819283|gb|BU499373.1|BU499373
EST:     TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG                         GATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
genomic: TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTGgtgagttttt ... attgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
EST: gi|149071910|gb|EE160296.2|EE160296
EST:     TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG                         GATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
genomic: TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTGgtgagttttt ... attgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
EST: gi|211533931|gb|FL079629.1|FL079629
EST:     TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG                         GATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
genomic: TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTGgtgagttttt ... attgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
EST: gi|21809641|gb|BQ667959.1|BQ667959
EST:     TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG                         GATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
genomic: TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTGgtgagttttt ... attgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
EST: gi|6342689|gb|AW165513.1|AW165513
EST:     TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG                         GATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
genomic: TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTGgtgagttttt ... attgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
EST: gi|211533928|gb|FL079626.1|FL079626
EST:     TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG                         GATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
genomic: TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTGgtgagttttt ... attgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
EST: gi|14243662|gb|BG841333.2|BG841333
EST:     TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG                         GATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG
genomic: TACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTGgtgagttttt ... attgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgatgtcctattgttgggatttgtttcattgctatttgggctatattgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTGTTGCTGATCCAACCTTTG
                                              ttgttcc  CT-rich tract
                                          tatattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatactagcaggatgcaaatccctatcttgtcatgactctgcatgcgatgtcctattgttgggatttgtttcattgctatttgggctatattgttccagGATTGGCTATCAAAGATTTTTGGCAGGTTGATGAGCGTACTATTGTTTTTGTTGCTGATCCAACCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT