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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaggtttgtggggctgagcaaacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 3
ctaggtttgtggggctgagcaa----acattgaaatctagggtccttgct--atgggtcttgccttgcagacatgttggatgttgac--tttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
        || |  || | |||     |||||    || | ||   ||||     | | ||    ||   |  ||  ||   ||||   | |||||||||  | |||||||||||| || || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||
--------gtagaactcaacaatgttgcattgttgccttgtgtgactgcttggcagatttttagctgagaaagtgcgggcctttgatcatgtgttcttttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 3
ctaggtttgtggggctgagcaaac-attgaaatctagggtccttgctatgggtcttgccttgcagacatgttgg-atgttgactttgt-tcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
        ||  | ||||  |    ||||   | | | ||  ||       || || | || ||   ||  |   ||| | ||      |   ||   ||||||||||||||||||||||||  |||||||| ||||| || ||||| || || ||||| || || |||||||| ||||| || || ||||
--------gtcag-ctgattagtttattgtgtttttgagtagtttt-----gtttttcttttcaacgattctattatgcttacaaaacataacttctaatcagGTCATTGTTGCTGATAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTCGAGCTTATTCGTCATG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 3
ctaggtttgtggggctgagcaaac-attgaaatctagggtccttgctatgggtcttgccttgcagacatgttgg-atgttgactttgt-tcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
        ||  | || |  |    ||||   | | | ||  ||       || || | || |||  ||  |   ||| | ||      |   ||   ||||||||||||||||||| ||||  |||||||| ||||| || ||||| || || ||||| || || |||||||||||||| ||||| ||||
--------gttag-ctaattagtttattgtgtttttgagtagtttt-----gtttttcttttcagcaattctattatgcttacaaaacataacttctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------------ctaggtttgtggggctgagcaaacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
                                                                                  || | | |       |  |  |  | | | ||  ||  |  | |   |  || |  | |   | |  | |   |   |  || |||  ||     ||||||| ||||||||||| ||||  |||||||| || || || ||||| || || ||||| || || |||||||||||||| ||||| ||||
gtaagtgggttatctatttgctcataatgttgtacttctgatgttcactcatgattttactgattttatacagatgccataacttgctatcatcctatatgtgataaataagatacagcata-tagaactaagtttgacttgataaagttctgccacaatatctctgtgttt----aatcagGTAATTGTTGCTGACAACTACTTCACTGGATCCAAGGACAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------ctaggtttgtggggctga--------gcaaacat--------tgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgt-tgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
                                                           ||   ||| |   | ||         || | |||        ||| |  || | | |    ||| |  ||    |||     ||    | | |   ||    |  || |   ||||||||||||||||||| ||||  |||||||| || || |||||||| || |||||||| || || |||||||||||||| ||||| ||||
gtaagagggttatctatttgctcataatgttatatttctgatgttcactcatgattttactgactttatacagatggcataacttgctatcatcctatatgtgataaataagatacagcatatagaactaagtttgatttgataaaagttctgccacaaaatctttgtttaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 3
-----ctaggtttgtggggctgagca---aacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
     || ||||  |     |  |     |   ||||||| ||       | | |   ||      |  |           |||| ||   | | ||  |   ||||||||||||||||||| ||||  |||||||| || ||||| ||||| || |  ||||| || || |||||||||||||| || || ||||
gttagcttggttgatatctttttgttcttagttttgaaatttattagttattcaacaagtacgatataactttggaacaatatgt-gatagtatgctggtctaatcagGTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 3
ctaggtttg--tggggctgagcaaacattgaaatctagggtcctt-gctatgggtcttgccttgcagacatgttgga----tgt-tgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
 | || |||  ||        |     ||    | ||   |  || | |||    |  |      | | |  |||||    | | |||   |   ||| |   ||||||||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| || || |||||||| ||||| || || ||||
gttggcttggttgatatctttctgttcttagtttttaaattttttagttattcaacaagtacaataaa-acattggaacaatatgtgatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 2
--ctaggtttgtggggctgagcaaacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
   | | | | |     |    |    || || | |   ||  || | |   ||         ||          |||| ||   |   ||| |   ||||||||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| || || |||||||| ||||| || || ||||
tggttgatatctttctgttcttagtttttaaattttttagttatt-caacaagtacaataaaacattggaacaatatgt-gatagtacgcttgtctaatcagGTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 2
ctaggtttgtggggctgagcaaacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
                         ||   ||  |      |||  |||  | |    ||     ||| ||   ||  |  || ||| | ||    ||||||  ||||||||||||||| ||||||||| |||||||| ||||| |||||||||||||| ||||| || ||||| || || || || |
------------------------gtttgtatacaaaa---ttgacatgcttttcaagtt-tgatcatatttt-tgaaggtttcgttttattct--tcagGTGGTTGTTGCTGATAACTATTTCACTGGCTCAAAAGAAAACCTCAAGAAGTGGATCGGTCACCCCAGGTTTGAACTTATTCGTCACG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 3
ctaggtttgtggggctgagcaaacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgac-tttgt-tcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
                  |    |||||||||       |  | | || |   ||     ||       ||   |  |||  ||| | | ||||   | ||||| |||||||||||||||| ||||||||||||||| || ||||| ||||||||||| || || |||||||||||||| ||||| || |
------------------gtttgcattgaaattcctatccgatacaatagtagtttatgcgcgatttgattaagtactgatgtttatatttttttttaccagGTGATTGTTGCTGATAACTATTTCACTGGTTCAAAGGACAACCTTAAGAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCACG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 3
ctaggtttgtggggctgagcaaacattgaaatctagggtccttgctatgggtcttgccttgcagac----atgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
    | || |    |  |  | | | |     | |  |    ||       | || |  || |  |     || |     ||||| |  ||  |||  | | |||| ||||||||||||||||  |||||||| || ||||||||||||| ||| ||||| || || |||||||||||||| || || ||||
----gattataccaccaaaaagaaaattttgaccaatgcgtctgtctgtcatgttacaatgtatccttgggtgcttatatttgacatgctttctttttgcttagGTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATG

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|6637013|gb|AW261285.1|AW261285
EST:     TCATCGGCTCGCACCTCGTGGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|149097834|gb|EE183762.2|EE183762
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|6194647|gb|AW146751.1|AW146751
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACCGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|6020952|gb|AW065880.1|AW065880
EST:     CATCGGCTCTCTACCTCGTGGACAGGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACCGGTTCAAAAGATAACCTGAAGAAG
genomic: CATCGGCTCGC-ACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|60672298|gb|DN475062.1|DN475062
EST:     TCATCGGCTCGCACCTCGTGGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|40334152|gb|CK368222.1|CK368222
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTT-CTGATAACTTTTTCACCGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|22473192|gb|BU037672.1|BU037672
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACCGGTTCAACAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|26558105|gb|CA830340.1|CA830340
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACCGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|148945878|gb|EC891170.2|EC891170
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|67016223|gb|CO444972.1|CO444972
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACCGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     AACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACCGGTTCAAAAGATAACCTGAAGAAG
genomic: AACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|21987903|gb|BQ779431.1|BQ779431
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACCGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|32165003|gb|CD670321.1|CD670321
EST:     CATGGAGAACGAGAAACACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
genomic: CATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
EST: gi|148951041|gb|EC896695.2|EC896695
EST:     TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcgc ... ttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG
                             tgttgac  putative branch site (score: 3)
                                   ctttgttcttttac  CT-rich tract
                                        ttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaggtttgtggggctgagcaaacattgaaatctagggtccttgctatgggtcttgccttgcagacatgttggatgttgactttgttcttttacgatcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA