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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacactgctgattcggttttttttcactttaaatgctcatgtgttttagttggatgtaacccatcaaccatactgcatatgattttgccatagcacataacattggcacattgttgaaaccaatttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT

Basic information

species Zea mays
transcript GRMZM2G093359_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 11
gtaagtacactgctgattcggttttttttcactttaaatgctcatgtgttttagttggatgtaacccatcaaccatactgcatatgattttgccata-gcacataaca-ttggcacattgttgaaaccaatttc-cacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT
                                                        |||||   ||  |   ||  | |||   |    || ||||| | |  |   |  |    | ||  || ||| | |||  | ||||||||||||  | || ||||| ||| ||||||||||| | |||||||||||  |||| || |||||||| ||||||||||||||||| || ||||||
----------------------------------------------------gtaaggatgcttcctgttttccg-attgc-cgtttcattaccatatgtatttgttagctttgtccttactgtaactattttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT
















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|60358486|gb|DN225459.1|DN225459
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|32937713|gb|CF042532.1|CF042532
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|211091998|gb|FL476411.1|FL476411
EST:     ATCAAAATG-TGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGKTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: ATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|60351022|gb|DN217995.1|DN217995
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|60401451|gb|DN234258.1|DN234258
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|16918483|gb|BM073768.1|BM073768
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATCGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|60338752|gb|DN205725.1|DN205725
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|60358733|gb|DN225706.1|DN225706
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|19058676|gb|BM737343.1|BM737343
EST:     AAAGATCAAAATGTTGCACTAATTGNCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGCGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|211167201|gb|FL456897.1|FL456897
EST:     AAAGWTCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|22490645|gb|BU050568.1|BU050568
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|24769868|gb|CA404997.1|CA404997
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|211126137|gb|FL125779.1|FL125779
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|94474487|gb|EB703445.1|EB703445
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCCCACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|87154062|gb|DY398851.1|DY398851
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|71424524|gb|DR806343.1|DR806343
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|5686716|gb|AI939809.1|AI939809
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|60397238|gb|DN230054.1|DN230054
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|5740098|gb|AI947788.1|AI947788
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|149106512|gb|EE188404.2|EE188404
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
EST: gi|86466217|gb|DY232590.1|DY232590
EST:     AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA
genomic: AAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 198

GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 126

GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 101

GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 133

GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCTgtaagtacac ... atttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgattttgccatagcacataacattggcacattgttgaaaccaatttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT
                 acataac  putative branch site (score: 133)
                                              tttccac  putative PPT
                   ataacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacactgctgattcggttttttttcactttaaatgctcatgtgttttagttggatgtaacccatcaaccatactgcatatgattttgccatagcacataacattggcacattgttgaaaccaatttccacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA