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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttattcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG

Basic information

species Zea mays
transcript GRMZM2G147884_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
gttattttattcagttcttgatgtgtatactttgacgttcaaaattttt--ctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
      ||  ||||||||| |||   ||  |||  |     | | ||||  |||| || |||||||  | |      ||||| || ||||||| || || || || | |||||| |||||||||||||| ||||| || || || ||||||||||| ||||||||||| ||||| |||||||||||||
--gtgcttgctcagttcttaatg---attttttacctccagagagttttaactttcatctgactattatatgcctttttttt-tgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 6
---------------gttattttattcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctt--taacctttttgtg-cagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
                 ||||  ||||| |||||| | | |||  ||   | ||    | | |   |  | |||| | || | |   |||  |  || |  ||||| || ||||| || ||||| || ||||| |||||||| |||||||||||||||  ||| ||||| || |||||||| ||||||||||||||||| || |
gtaaaggcatttgcttatattccattca-ttcttg-tctttatttttcctcctttctcaatgtagatgaaattgaatttgttttgcataatgtcattatttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 6
-----gttattttattcagt-tcttg-atgtgtatactttgacgttcaaaatttttct--ttgatttgactatgctct----ttaaccttt-ttgt-gcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
        ||  ||||   | ||||| |||  |||  |||| |   |  | | |||||  |||  ||   | |  |||    ||||  ||| ||||  |||||||| ||||| ||||| ||||| || ||||||||||| || |||||||| ||||||||||| ||||| |||||||| || ||||| ||||||||||| |
gtattagaataatatttgttctcttgtatgcttatcatttgtcac-cgtattctttctgattggattcctttttatctgaggttaatgtttgttgttacagGGATGTGATTGTTTGGGATACATCAAGTATTTTGATGCTCACTTCACAAATTTCACTGGTGGGGTGGAAACAATTGAAAATTGTGTATGTTTGCATGAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
-----------gttattttattcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
            |  | | ||| |||     ||   | | ||||  |  |  | ||    ||   |||| | | ||||   | || || |||  ||||| || ||||| || ||||| || || || |||||||| || ||||||||||| | ||| ||||| || ||||| ||||| |||||||| |||||||| |
gtcaaggcattttcttctaatttagtctcaaattactctcctttctctatgtagatgaaactaaaattt-attttgcttggtgacattattg--cagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G09290.1 (Glycine max), 3'ss of exon 5
----------------gttattttattcagttcttgatgtgtat-actttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
                 ||||  | |||| |  || || | ||  |  ||    ||    |||    ||  ||  | |||   ||   ||| ||| | ||||||| || ||||| ||||||||||| ||||| |||||||| ||||||||||| ||||||||||| || ||||||||||| || ||||| ||||||||||| |
gtttgagaaacctatatttatccttttcaatgttttatatttaccaagttcctctttctgattaagtttcaatgagtctaaagtc---aacatttgt-tgcagGGGTGTGATTGTTTGGGCTACATCAAATACTTTGATGCTCATTTCACAAATTTCACTGGTGGAGTTGAGACAATTGAAAATTGTGTATGTTTGCATGAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 6
--------gttattt-tattc-agttcttgatgtgtatactttgacg--ttcaaaatttttctttgatttgactatgctctt--taacctttttgtg-cagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG-
         ||  || ||||| ||   ||  ||| |  | |||| |   ||    | | |   |  | |||| | || | |   |||  |   |||  ||||| |||||||| || ||||| || ||||| |||||||| || ||||||||||||  ||| ||||| || ||||||||||||||||||||||||||||| | 
taaatgcatttgcttatattccagacattcttgtcttcattttgcctcctttctcaatgtaaatgaaattgaatttgttttgcataatgtgactgtttcaggGCTGCGATTGTTTAGGCTATATCAAATACTTTGATGCGCACTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAGAACTGTGTTTGTTTGCATGAAGA

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 6
gttattttat-tcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
    ||| |  |||||| ||  | ||      ||  |  ||| |  |    ||   ||| ||          || |  ||| |  |||| || || ||  |||| |  || || || || ||||| ||||||||||| |||||||| || || || |||||||||||||||||||| |||||||| |
---gtttgacatcagttttttttttggtgttcttaccactcagatctcagtttgtgtttaac----------aatcggtttttatagGGGTGTGACTGTCTGGGATCTATCAAGTACTTCGATGCCCATTTCACAAATTTCACTGGAGGAGTTGAAACAATTGAGAACTGTGTTTGCTTGCATGAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------gttattttattcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
                                        |||| |  |   |   |  |   || |    |    ||| |||  || |||  |||   | || || |   |  | | |||||||| || |||||||| || || || || || ||||| |||||||| ||||| |||||||||||| | || |||||||| || |||||||| |||||||| |
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcat-gtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 6
------------gttattttattcagttcttgatgtgtatactttgacgtt-caaaatttttctttgatttgactat----gctctttaaccttt--------ttgtg----cagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
             ||  || ||  | || |   |   | |  ||| || ||    || ||| || |  ||||| | |    | ||||   | ||         || ||    |||||||| |||||  | || |  || ||||| |||||||| || || |||||||||||||| ||||| || || ||||| || ||||||||||||||||| |
gtctataaaactatttcttcatgtaattgtccttaaattttattttaccttgtggaactttactattgtttgaatctaaaagatcttctgctttaaaatgaaattatgaccacagGGATGTGATTGTCTAGGGTTTATCAAATACTTTGATGCCCACTTTACAAACTTCACTGGAGGTGTTGAAACGATTGAAAATTGTGTTTGTTTGCATGAAG

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|91873704|gb|EB403661.1|EB403661
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|211285877|gb|FL038890.1|FL038890
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|211285882|gb|FL038895.1|FL038895
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|67028492|gb|CO457241.1|CO457241
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|211180988|gb|FL326379.1|FL326379
EST:     TTGATGCTGGAGAAGATGGACTTGNAAAAAATGCTCATTCTCTTAANAAG                         GGATGCGATTTGCTTGGGCTACATAAAATATTTTTGATG
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATT-GCTTGGGCTACATAAAATATTTT-GATG
EST: gi|67010284|gb|CO439033.1|CO439033
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|211285878|gb|FL038891.1|FL038891
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAAT-TTT-GATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|31348944|gb|CD433301.1|CD433301
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|47961763|gb|CN844472.1|CN844472
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|18661626|gb|BM501497.1|BM501497
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|211285879|gb|FL038892.1|FL038892
EST:     TGATGCTGGAGAAGAATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TGATGCTGGAGAAG-ATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|211285883|gb|FL038896.1|FL038896
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
EST: gi|211285881|gb|FL038894.1|FL038894
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAA
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAA
EST: gi|211285880|gb|FL038893.1|FL038893
EST:     TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAG                         GGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC
genomic: TTGATGCTGGAGAAGATGGACTTGGAAAAAATGCTCATTCTCTTAAGAAGgttattttat ... ttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG
                                    ctttaac  putative branch site (score: 3)
                                  ctctttaaccttttt  CT-rich tract
      ttcaaaatttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattttattcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA