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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttgctttctctttgcatctatagatgcatattctactttcttttgaaatttactaagctgtgaggtagtcagaaagctgacactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG

Basic information

species Zea mays
transcript GRMZM2G178859_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 3
gttcttgctttctctt-tgcatctatagatgcatattctactttcttttgaaatttactaagctgtgaggtagtcagaaagctgacactggaactaaacat-gcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG
|||| | |    |||| |  || |||     ||| || |   || |||| ||  |   |    |  |  || |  | |   |||  | |  | || ||||  | ||||  |||||||||||| ||||||||||||||||||| |||||||| ||||||||||||||| |||||||||||||||| || || || |||||||||||||||||||| |||||||||||||
gttcgtacaagatcttctctatttatctgcacatgttatgtgttgttttaaatgtgtttcgtttcagtagttggtatagtactgttattacatctgaacaccgtaaaattttggcaaggtttctgcagGCTAATGGCTTGGCGGCTGGGCTCGCAGCTTCTAATCTTATTCTGTATGCATTTGTATACACACCATTGAAGCAAATACACCCTGTAAATACATGGGTTG

upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G43980.1 (Glycine max), 3'ss of exon 5
gttcttgctttctctttgcatctatagatgcatattctactttcttttgaaatttactaagctgtgaggtagtcagaaagctg-acactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG-------------
                                                                           |     ||      || |||||   |||       || |||||||  | ||| |||||   || || ||||||||||| ||||| || ||  |||||||||||||||| ||||| || |||||||| || || |  || ||||||||||| |             
---------------------------------------------------------------------------gtgctttgtgtggagggactaacattgctgctttatgacaaggttattccagactaatatgttagCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCTCGTAAATACATGGGTGGGAGCTGTTGTCGG

upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 3
------------------gttctt-gctttctctttgcatctatagatgcatattcta--ctttcttttgaaatttactaagctgtgaggtagtcagaaagctgacactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG
                  || ||| | |   | | ||| | | ||| || |  || ||  | |     || | ||     |  |||  | |   |    ||  ||    || |||||   ||||      || |||||||  | ||| | |||   || || ||||||||||| ||||| || ||  |||||||||||||||| ||||| || |||||||| || || ||  | ||||||||||| |
gtattgaaacaaatttgcgtactttgttgattgtatgcttttctag-tgtaacttgtaaacctatgactggatttcttataattgtttgatgtgctttgagtgga----gggactaacattgcagctttatgacaaggttattccagACCAATATGTTAGCTGCTGGGCTTGCTGCTTCCAACCTAATTCTGTATGCATTTGTATATACACCCTTGAAGCAGATTCATCCCATAAATACATGGGTGG

upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 3
gttcttgctttctctttgcatctatagatgcatattctactttcttttgaaatttactaagctgtgaggtagtcagaaagctgacactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG
                        |  |||  | || |  ||| | |   | ||   |    | |||    || |   ||  ||   |||| |||||| |          | |||||||  ||||| |||||   ||||| ||||| |||||| || | |||||||| || ||||| ||||| ||||| |||||||||||| | |||||| | |||||||||||||
-----------------------gtgaatgtttgtttt--tttatatgtgatttctttgttttatgaatgggtgattgaga-gattatggatctaaacttttgcttccacgacaaggttattgcagACTAATATGTTGGCTGCTGGACTTGCATCTGCCAATCTTGTACTTTATGCGTTTGTTTATACTCCGTTGAAGCAACTTCACCCTATCAATACATGGGTTG

upper sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gttcttgctttctctttgcatctatagatgcatattctactt--tcttttgaaatttactaagctgtgaggtagtcagaaagctgacactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG
                      |  | ||  || |  |||  |  ||| || || | |  |  ||  |||   |||  ||   | |    || ||    |  ||  |||     |  |  | | |     || |||||||  ||||||||||    |||||||| ||||||||||||||||||||| |||| || || ||||| || || || ||||||||||| || || ||||| || |||||||
gtggtgccataaactctatcgccccgtttcttcatgtcattcaatgatacaaatgcaaaataatcccttgttgtttgata---tcttgaatattctagtaattgg-actcatgttgcatgttcta-----tgacaaggttgttgcagGCTAACATGTTGGCAGCGGGGCTTGCAGCTTCTAATCTTCTTCTTTACGCCTTTGTATACACTCCATTGAAGCAAATTCATCCAGTTAACACCTGGGTTG

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|71329079|gb|DR801247.1|DR801247
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGTTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
EST: gi|31361673|gb|CD446030.1|CD446030
EST:     TGTGGGCTACAAGTGTTGGAGTTGCTGGAACAGCTTTGCTGGCATGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
EST: gi|211400285|gb|FL144411.1|FL144411
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGAATGC
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGC
EST: gi|71329076|gb|DR801246.1|DR801246
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGTTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
EST: gi|211400287|gb|FL144413.1|FL144413
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
EST: gi|71443478|gb|DR824528.1|DR824528
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
EST: gi|71320010|gb|DR796769.1|DR796769
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
EST: gi|71318333|gb|DR795929.1|DR795929
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
EST: gi|76921322|gb|DV168542.1|DV168542
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
EST: gi|78081008|gb|DV509420.1|DV509420
EST:     TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGTTGGCCTGGAAG                         GCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA
genomic: TGTGGGCTACAAGTGTTGGAGTTGCAGGAACAGCTTTGCTGGCCTGGAAGgttcttgctt ... gtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagaaagctgacactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG
                   aactaaa  putative branch site (score: 2)
                               aaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttgctttctctttgcatctatagatgcatattctactttcttttgaaatttactaagctgtgaggtagtcagaaagctgacactggaactaaacatgcaaaaaattggcaaggtttgtgcagGCTAATGGCTTGGCAGCTGGGCTTGCAGCTTCTAATCTTGTTCTGTATGCATTTGTGTATACGCCGTTGAAGCAAATACACCCTGTTAATACATGGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA