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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcaaaccactcttgacttttttttgtctttcggctttctcttgctatggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG

Basic information

species Zea mays
transcript GRMZM2G165351_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g51430.1 (Oryza sativa), 3'ss of exon 9
gtactcaaaccactcttgactttt----ttttgtctttcggctttctcttgctatggcctttgttgataatattt---agttgaggtacgagttttgtttgt---------catgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG
||| || | |  ||||||||||||    || |   |   || | |      | || ||   | || ||  || ||    || |  || | |||| | |||||         ||||| ||||||||||| ||||| ||| ||||||||||| | ||||| ||||||||||||||| |||||||||||||||||||||||||||||||||| |||
gtaatctagctgctcttgacttttgactttctacatgatggatgttaagctccattgcaagttttcattttactttagcgtggttgttcaagttatctttgtaactgaggccatgaacagGTGGGTTCAGTTCTCCTCAGCTGTGCCTTCTTTTATGACATCTTCTGGGTGTTTGTCTCCAAGAGATGGTTTCATGAGAGCGTGATGATCGTG

upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G07610.1 (Glycine max), 3'ss of exon 10
gtactcaaaccactcttgacttttttttgtctttcggctttctcttgctatggcctttgttgataatatttagttgaggtacgagttttgtttgtcatga-tcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG
     || | |  |   ||  |   ||||    | |    |      || |     |     | || |  ||  |||   ||   |    |||    ||| |||||| ||  | ||||||||| | ||||||||||| ||||| ||||||||||||||| |||| ||  | ||||| |||||||| |||||||| |||
-ctgacagatcgttgaagagatagctttgc---tggatactactgaacttttattatgaacaaaaacaccta-ctgactgacatataccattttctctgaatcagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATCTTCTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------------------------------------gtactcaaaccactcttgacttttttttgtctttcggctttctcttgctatggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG
                                                                                                    || | || |    || |||   | |   ||  || ||| || ||  | ||||| ||  ||| |   |       |       || |||  |||| | |||| ||  | ||||||||| | ||||||||||| || || ||||||||||||||| |||| ||  | ||||| |||||||| |||||||| |||
gtgattatacattacttaagcttgtattttgcacaatcacctacttaggttgtttgttatattcttgaaaattaagcttgggatgcataaaggggacctccatatcagtga-aacatttaaatatggatctactgtctattact--gaccttttttattaacaaaaaacactaatttatacatt-ttttccatg-taagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G46760.1 (Glycine max), 3'ss of exon 9
gtactcaaaccactcttga-cttttttttgtctttcggctttctcttgct-atggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG
 |  | | |   |  |  | |  ||   | |   ||  |  | | || || |     ||| || | || |   |  | |  ||    |||| |   |     | |||| ||  | ||||||||| | ||||||||||| || || ||||||||||||||| |||| ||  | ||||| |||||||| |||||||| |||
-tttttatatttcagtgaaacgattaaatatggatctacagtgtattactgaccatttttattaacaaaaaaga-ctaatttatacattttttccat----gtaagGTCGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G01100.1 (Glycine max), 3'ss of exon 9
gtactcaaaccactcttgacttttttttgtctttcggcttt---ctcttgctatggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG
     |||| || |   ||| |   ||||           |   || ||  ||||  |         |     |    ||  ||    |||| |   ||   ||||||| ||  | ||||||||| | ||||||||||| ||||| || || ||||||||| |||| ||  | ||||| |||||||| |||||||| |||
---gacaaatcattgaagacatagctttgctggatactactgaacttttattatgaacaa-aaaagcacccactgaccgacatatacctttttt---tctgaatcagGTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATTTTTTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTG

upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 7
lower sequence: AT1G63690.2 (Arabidopsis thaliana), 3'ss of exon 9
gtactcaaaccactcttgacttttttttgtctttcggctttctcttgctatggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG----
           | |  |      | ||| |   ||  | |    || | |   | |||  ||| || |||   |  ||  || | | |   |||     | ||||| ||  | ||||||||| ||||||||||| |||| |||||||||||||||||| |||||||||  | ||| || || ||||| ||||||||     
--------gtaatttcttgaacgtatttatacgtcatcgtagagtttccaaaactttt--tga-aagatt--ataaagccac-attatcacttg----aaacagGTCGGGACAGTTCTTCTCAGCTGTGCCTTCTTGTACGATATCTTCTGGGTGTTTGTCTCCAAGAAGTTGTTCCACGAAAGCGTAATGATTGTCGTAA

upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 7
lower sequence: AT1G63690.1 (Arabidopsis thaliana), 3'ss of exon 9
gtactcaaaccactcttgacttttttttgtctttcggctttctcttgctatggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG
           | |  |      | ||| |   ||  | |    || | |   | |||  ||| || |||   |  ||  || | | |   |||     | ||||| ||  | ||||||||| ||||||||||| |||| |||||||||||||||||| |||||||||  | ||| || || ||||| |||||||| 
--------gtaatttcttgaacgtatttatacgtcatcgtagagtttccaaaactttt--tga-aagatt--ataaagccac-attatcacttg----aaacagGTCGGGACAGTTCTTCTCAGCTGTGCCTTCTTGTACGATATCTTCTGGGTGTTTGTCTCCAAGAAGTTGTTCCACGAAAGCGTAATGATTGTC

upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 7
lower sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 9
gtactcaaaccactcttgacttttttttgtctttcggctttctcttgctatggcctttgttgataatatttagttgaggt-acgagttttgtttgt-catgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG
|     | ||   |    | |  ||| || |  |    | |      | |    || |  | | |||||| ||||  | | ||   ||    |  | | | | ||||| || |  ||||||||| ||||||||||| ||||||| ||||||||||| ||| | || ||  | ||||| | ||| |||||||||||||||
gctggtagacggatac--aatcatttctgccaatg---tatagaagaccaatctctataataacaatatt-agttatgatgactcattgaactcttacgtaaacagGTCGGGTTTGTTCTTCTCAGCTGTGCCTTCATGTATGACATCTTCTGGGTTTTTGTTTCAAAATGGTGGTTCCGTGAAAGCGTGATGATTGTG

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|67025992|gb|CO454741.1|CO454741
EST:     TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
genomic: TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|32843028|gb|CD982709.1|CD982709
EST:     GTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
genomic: GTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|74234147|gb|DT642061.1|DT642061
EST:     AAATTGTGAGAGTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
genomic: AAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|67024697|gb|CO453446.1|CO453446
EST:     TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGTATTATATCTTCTGGGTG
genomic: TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|32848049|gb|CD987730.1|CD987730
EST:     ACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGCATGATATCTTCTGGGTG
genomic: ACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|67017568|gb|CO446317.1|CO446317
EST:     TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGTATGA-ATCTTCTGGGTG
genomic: TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG
        tgttgat  putative branch site (score: 4)
      tttgttgataatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcaaaccactcttgacttttttttgtctttcggctttctcttgctatggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG