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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC

Basic information

species Zea mays
transcript GRMZM2G123140_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggat-gcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC
||| |     ||  |  ||   |||  |||    |  |     ||   |  |   | ||||  |||    ||  |||    | ||    || |  ||    |     ||| | ||| | |   ||| |   |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||||||||| 
gtacggttttcatctccatcttctt--cttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgt-gcatgcatc-catccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT

upper sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 2
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacata----cgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC
                                    || |    |    ||  | |||  | |  || || ||   || |||  | |  |     ||    ||  |    || || |    |  ||        |||  |||||||||| ||||| ||||| || || |||||| ||||||| |||||||| ||  |||| || ||||| |||||||||||||||||||||||||||
------------------------------------tagatctctctcttttgtttcctttgtgata-aaactgaaactgatcaaggttttaatttgttgttgttcattgtttcatgtgtaatgtaacatttggcagTTTGTTCAAGGAATGCCCACACCCTGATGATAAGCAGAGGCTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 2
gtaagacacacacatatatacgcttgccttttcatatataataataatcttctt-ctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC
                              |  ||||  | |  ||   || ||  |    ||  ||  ||  ||  || |     |   |  |  |  || |       | |   |  |     |     |||  |||||||||| || || |||||||| || |||||| | ||||| |||||||| ||  |||| || ||||| |||||||||||||||||||||||||||
-----------------------------ataaatattaattgttagcattattatttttgtaagttgaaaattcgaactgcaatcttttttcctttatcactaa-----actaaccttatatttttttggcagTTTGTTCAAGGAATGTCCACACCCGGATGATAAGCAGAGACTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC

upper sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
lower sequence: EFJ37532 (Selaginella moellendorffii), 3'ss of exon 1
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC
                                                                                 | | |||| | | |  ||| ||    | | |   |   |  | | |   |||| ||||||||||||| || || || ||||| |||||||| | | ||||||||| |||||| || ||  | || || || |||||||||||||||||||| 
----------------------------------------------------------------------------gtaagtac-tgcaagccgagagca-tgatgagaacttatctttcttcgtgc---cagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT

upper sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 2
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacgg-atgcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC
                                                            ||    ||    | |   |   | |  |  ||| | |    | ||  |   ||            | ||| |||  ||||||||||||||||||| ||||| ||||||||||||| | |||| |||| |||||| ||  |  | || || || |||||||| ||||||||||| 
-----------------------------------------------------------gtaagagattggttttggtgttgttctcgattggaagtcctcaaggtggattttttcttcgttttct-cgcgcagCTTGTTCAAGGAGTGCCCGCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAAT

upper sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
lower sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC
                                                                                 | | | || | | |  ||| ||    | | |   |   |  | | |   |||| ||||||||||||| || || || ||||| |||||||| | | ||||||||| |||||| || ||  | || || || |||||||||||||||||||| 
----------------------------------------------------------------------------gtaagtac-tacaagccgagagca-tgatgagaacttatctttcttcgtgc---cagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT

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|78084627|gb|DV513020.1|DV513020
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATAGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|50324011|gb|CO519137.1|CO519137
EST:     ACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: ACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|71764164|gb|DR962101.1|DR962101
EST:     CCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: CCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|148938577|gb|EC882901.2|EC882901
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCAGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|50330271|gb|CO525397.1|CO525397
EST:     GGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: GGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|78083048|gb|DV511441.1|DV511441
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|50322570|gb|CO517696.1|CO517696
EST:     ACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: ACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|50323712|gb|CO518838.1|CO518838
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|76294065|gb|DV033633.1|DV033633
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|76291558|gb|DV031126.1|DV031126
EST:     AACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|50335383|gb|CO530509.1|CO530509
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|76922345|gb|DV168961.1|DV168961
EST:     CACGGCACACCAGATCCAGCAGATGGAAGC                         GCTG-TCNAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGA
genomic: CACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTC-AAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGA
EST: gi|149087104|gb|EE176643.2|EE176643
EST:     AAGAAACAGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|148953385|gb|EE152879.2|EE152879
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|71426041|gb|DR807091.1|DR807091
EST:     GGCACCCCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAC
genomic: GGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|50333731|gb|CO528857.1|CO528857
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|71758544|gb|DR956481.1|DR956481
EST:     AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: AAGAAACGGTACCACCGCCACACGGCACACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|38687296|gb|CK144327.1|CK144327
EST:     CACCAGATCCAGCAGATGGAAGC                         GCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: CACCAGATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
EST: gi|71317347|gb|DR795368.1|DR795368
EST:     ATCCAGCAGATGGAAGC                         GCTGTTCAGGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG
genomic: ATCCAGCAGATGGAAGCgtaagacaca ... atacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacatacgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT