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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcctgtccatatcttataatttggtttcacaaaatcttaattcttaattaatctgaatctgatagtcagctcattcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG

Basic information

species Zea mays
transcript GRMZM2G121790_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 5
gtatggcctgtccatatcttataatttggtttcacaaaatct-taat-tcttaat-taatctgaatctgatagtcagctcattcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG
|||||  |  | ||    | ||| |||  |  |      |    | | ||| ||| ||| |||| ||| |   |    |  ||  | |||||| ||||| || ||||||||||| || ||||||||||||||||| || |||||||||
gtatgttcatttcacgcttgatattttaataacctgtggttaacagtatctgaatataagctgattcttactttatattggttt-taatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAAATGTTG
















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|19770441|gb|BQ035162.1|BQ035162
EST:     AAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: AAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|148952787|gb|EC898773.2|EC898773
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|148932530|gb|EC876330.2|EC876330
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|76287882|gb|DV027450.1|DV027450
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|211251114|gb|FL353291.1|FL353291
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|71441697|gb|DR822747.1|DR822747
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|32855414|gb|CD995095.1|CD995095
EST:     AGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: AGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|211298028|gb|FL233897.1|FL233897
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|33098911|gb|CF058871.1|CF058871
EST:     ACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|94476799|gb|EB705757.1|EB705757
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|149112787|gb|EE191425.2|EE191425
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|71430638|gb|DR811688.1|DR811688
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|211326797|gb|FL341548.1|FL341548
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|31351371|gb|CD435728.1|CD435728
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|71443964|gb|DR825014.1|DR825014
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|211298026|gb|FL233895.1|FL233895
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTG-AAMCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|148931707|gb|EC874917.2|EC874917
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|76922778|gb|DV169169.1|DV169169
EST:     ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|20300401|gb|BQ163344.1|BQ163344
EST:     AACC-CAAAATCTTTTG                         GTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: AACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA

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), 49 (downstream exon)
Score: 187

ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

ATATTTCGAGGCTTAGCCTATATTCACACAGTACCTGGAGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTGgtatggcctg ... ttcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaatcttaattcttaattaatctgaatctgatagtcagctcattcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG
                                         ctcattc  CT-rich tract
        ttaattcttaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcctgtccatatcttataatttggtttcacaaaatcttaattcttaattaatctgaatctgatagtcagctcattcattatagGTTGATCCACTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA