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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA

Basic information

species Zea mays
transcript GRMZM2G004528_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 9
gtaa-gccttttcgcctgcattaattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA
|||  |||  ||  ||   ||   |||   ||| | |  |||      || |  | |   | | | ||   |   |  |     ||| |  ||||||||| || |||||||| ||||||||||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| |||||||| ||||||||||
gtactgcccattaaccgttat--gttctttcat-gatataccaa---ctgatttacttatgtcacgaaaaattcgtctc-----ctgga--acagGTTCCTCCTGGCACACCAGTGGTGAACGCCCTGGCAAAGCAGAGGGCAATGCTTGAGAACATCATGAGGGCCTGCGTTGGGCTGGCCCCCGAGAACAACA

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 3'ss of exon 8
----gtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaat-------gacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA
    ||       | |  ||| | |         | || |        || || |  |  ||| | | |   ||| | | || |||  |   |        ||||||||| || |||||||| ||||||||||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| |||||||| ||||||||||
gtgagtgcatacatgcatctgtactgcccatta-accgttatgttctttcatgatata--ccaactgatttacttatgtcacgaaaaattcgtctcctggaacagGTTCCTCCTGGCACACCAGTGGTGAACGCCCTGGCAAAGCAGAGGGCAATGCTTGAGAACATCATGAGGGCCTGCGTTGGGCTGGCCCCCGAGAACAACA

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
---------------------------------------------------------------------------------------------------------gtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgct-ccaatccagccgctaatcttctcttacaaaacctgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA
                                                                                                         || |     ||   | |    | ||||    |  |  |    ||| ||  |  |||   ||  |  ||  ||  || |||| |      |  ||||||||||| || ||||| |||||||| ||  |  |||||||| | || |||||||| ||||| ||||||||||| |||||  ||||||||||||| ||||
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtga-atttcccttttttccccttatcatttttttatcaaaaaagttggcaaggtta-ctcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 6
gtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgc-tccaatccagccgctaatcttctcttacaaaacc--tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA
||||| ||  |       ||| ||    |  ||  || |     |||  | |     ||      |||  ||||   | | ||    | ||| |||||||||||| || ||||| |||||||| ||  |  |||||||| | || |||||||| |||||| |||||||||| |||||  | || || ||||||||||
gtaagtctaatactaccgattcataattgt-tcaatgaattaattctctcatttccccctttaattaaatttctgaaatacaattattaaattacagGTTCCACCGGGTACACCAGTGGTGAATGCGTTGTCAAAGCAGCGAGCTATGCTGGAAAACATCCTGAGGGCTTGTGTTGGATTAGCTCCTGAGAACAACA

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA05G31450.3 (Glycine max), 3'ss of exon 9
--gtaagccttttcgcctgcattaattc--cggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA
   |||  ||          | |  |||   |   |   |    |   ||   ||  |||  |    || |  | |  |||       | ||| |||||||||||| || ||||| |||||||| ||  |  |||||||| | || |||||||| |||||| |||||||||| |||||  | || || ||||||||||
gtctaatactaccgattcataattgttcaatgaattaattctctcatttccccctttaattaaatttctgaaatacaattat------taaattacagGTTCCACCGGGTACACCAGTGGTGAATGCGTTGTCAAAGCAGCGAGCTATGCTGGAAAACATCCTGAGGGCTTGTGTTGGATTAGCTCCTGAGAACAACA

upper sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 9
-----gtaagccttttcgcct-gcattaattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA
       |||  ||  |  || |  |  | |  |  |    || |  |    ||| |   ||   |  | |       | |         | ||  |||||||||||| ||||| || |||||||| || || || |||||| |||| ||||| ||||||||  | |||||||| |||||  |||| || ||||||||||
gacatcaaagttttaccttcttgtttggaatatgcgaggaatgtagagttagttgatagcattatgatgttgtaacgttttgttggtgtattaaaaacagGTTCCACCAGGCACTCCAGTGGTGAATGCACTGGCGAAGCAGCGGGCAATGCTCGAGAACATACTAAGGGCTTGTGTTGGATTGGCTCCCGAGAACAACA

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|13388668|gb|BG462341.1|BG462341
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|6022235|gb|AW067163.1|AW067163
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|6021982|gb|AW066910.1|AW066910
EST:     CCTTCCACCCGGTGGCCNCCATCCTTAGCTACCTCACCAAGGCACCNCTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|110941538|gb|EE161695.1|EE161695
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|110217273|gb|EC899171.1|EC899171
EST:     CTTTCCACCCGGTGGCCACCATCCTTAGGTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|13388670|gb|BG462342.1|BG462342
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCG
EST: gi|6022029|gb|AW066957.1|AW066957
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|6022307|gb|AW067235.1|AW067235
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|6021766|gb|AW066694.1|AW066694
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|71756431|gb|DR954368.1|DR954368
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|91871596|gb|EB401553.1|EB401553
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|71771141|gb|DR969078.1|DR969078
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|6022274|gb|AW067202.1|AW067202
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|6022096|gb|AW067024.1|AW067024
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|32854168|gb|CD993849.1|CD993849
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCGCCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|149071426|gb|EE159821.2|EE159821
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGGGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|13515776|gb|BG518052.1|BG518052
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|13515973|gb|BG518249.1|BG518249
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|60397539|gb|DN230355.1|DN230355
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|148952105|gb|EC897897.2|EC897897
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|21621348|gb|BQ619354.1|BQ619354
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|6021614|gb|AW066542.1|AW066542
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|32854394|gb|CD994075.1|CD994075
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCGCCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|148928580|gb|EC873008.2|EC873008
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
EST: gi|148936902|gb|EC881051.2|EC881051
EST:     CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG                         GTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG
genomic: CCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTGgtaagccttt ... tgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA
                                ctcttac  putative branch site (score: 3)
                                   ttacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgctccaatccagccgctaatcttctcttacaaaacctgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA