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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttgacattgtagcttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG

Basic information

species Zea mays
transcript GRMZM2G064695_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttgacattgtagcttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG
                                    | ||    |    ||||||| ||||       |  ||||||   ||| |  |||   | ||     |   |  | | || | |    ||   || || || || |||||     ||||||||||||| ||||||||  ||||||| ||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||||||||||
----------------------------------aatctgtttgttggaatccatgctaaatt-----gttattttgtttttgcatgttatgcttcc-----cagtttggtcatttataaacttt---ttatataacttgtattc-----agGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 9
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgcca--ttttgacattgtagcttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG
                                                     || |||||   |      |  |||||  |   |   | |||   |  || |     |||  ||||    | |  || |  |  ||||   ||   |  ||||| || || || ||||| ||| ||||| | ||||| | ||||||||||||| | || ||||||||||| || || ||||| |||||||| ||||||||||
-----------------------------------------------aagattatattaaatttttcttttagtttttgctagattccttcaatgatctacatgttatgatgtttttg----ttcacatttaatgcaatt---atgtaaatcagGTGGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGGGGTATAATGAAGTGTGATGTTATAGCAAGTG

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 9
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccc-tgacgccattttgacattgtagc--ttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG
                                                     || |||||    |       ||||  | | |   |  ||||| | |  || |     |||  ||||    | | ||| |  |  ||||   ||   |  |||||||| || || ||||| ||| ||||| | ||||| | ||||||||||||| | || |||||||||||||| || ||||| |||||||| ||||||||||
------------------------------------------------agattatattaaaaaaattgtatagttttttcctagatacctttaatgttctccatgttatgatgtttttg----ttcatatttaatgcaatt---atgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 9
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttgacattgtagcttaatttgccgcaggcgcatatgcctttgacagtg-cttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG
                                                     |     |||| |    |  | || || ||   |    | |    | |     |      ||| | || |  || | |   |||||             |||| |||||||| |||||||||||||| || || |||| |||||| |||||  | |||||||| |||||||| || ||||||||||||||||| || ||||
---------------------------------------------------gtaaaaggaaccttctttctttcttcacttttggg----aatcattggaatgaaaaccaattttaatagaggtttgtgtcaaaaaata------------agGTGGTGGAAGCGTTTAAGATACTGACATCGGACGATAAAGTGAAAGCAATCTTGGTGAACATATTTGGTGGGATAATGAAATGTGATGTGATTGCTAGTG

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 9
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttg-acattgtagcttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG
                                            |||   ||  | |   ||  ||| ||  ||    |||    |  ||| | ||    |     | ||       | | |  |||  |  ||||     |||   |  ||||| |||||||| || || ||| ||||| | |||||||  || || |||||| |||||||||||||||| || || |||||||||||  | ||||||||||
--------------------------------------------tcttgctctttctctcacattgatgcacttaaatacaactcaagttactgtgttataaataaagatat-----atatttattaattcttaaa----ttatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttgacattgtagcttaatttgccgcaggcgcata-tgcctttgacagtgcttatcttgtaa-aatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG
                                                   |||||| |    ||  |     | |    |||| |||   | ||  |||   |  |  |   || |    |  ||| |        || | |    | | |||||||||||||||||||| || |||||||| ||    |||||||| || ||||| ||||||||||||||||| || ||||| |||||||| || ||   ||
---------------------------------------------------ccatgtaatcaactaccatagctgtag--ttgttgct-gttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG

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|18162086|gb|BM331925.1|BM331925
EST:     GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
genomic: GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
EST: gi|5714240|gb|AI944225.1|AI944225
EST:     GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
genomic: GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
EST: gi|32846416|gb|CD986097.1|CD986097
EST:     TACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
genomic: TACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
EST: gi|148951068|gb|EC896727.2|EC896727
EST:     GCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
genomic: GCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
EST: gi|60398611|gb|DN231427.1|DN231427
EST:     GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
genomic: GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
EST: gi|32940144|gb|CF044963.1|CF044963
EST:     ACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
genomic: ACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
EST: gi|211240437|gb|FL261944.1|FL261944
EST:     GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
genomic: GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
EST: gi|211240439|gb|FL261946.1|FL261946
EST:     GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
genomic: GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT
EST: gi|60354613|gb|DN221586.1|DN221586
EST:     GTACGCCCGCCAATTTTCTTGACGTCGGTGGAAGTGCATCAGAGGGGCAG                         GTTGTGGAAGCTTTTAAGATACTGATTTCAGATGATAGAGTGAAGGCAATT
genomic: GTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattg ... ttctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG
              ctttgac  putative branch site (score: 4)
                                       tttctattctatcc  putative PPT
                          ttatcttgtaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttgacattgtagcttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG