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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgatttatcgcaactgtgtcatctcaacacgtatcctcgtttcgaccttcaagctaaccgcccagcaatgtgttgttcttccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGATGGCTAGGAAAGGTGGGGAGGATGTTGACGAAAAACTGGGAGACCATTT

Basic information

species Zea mays
transcript GRMZM2G137930_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 8
gtaagttgatttatcgca--actgtgtcatctcaacacgtatcctcgtttcgacct---tcaagctaaccgcccagcaatgtgttgttcttccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGATGGCTA--GGAAAGGTGGGGAGGATGTTGACGAAAAACTGGGAGACCATTT
|| |||   |   | |||  | |    || |  |      ||  | || |  |      ||||||| ||  |  | | |||| |  |  | |||| ||  |||| || |||||||| |||||||| |||||| |||||||||||  || ||  |  |   |||  |   ||  |||||||||||||||    |||||  ||| 
gtgagtacttcacttgcataagtactacaacatactgtacatgtttgtgtaaaatcacatcaagctgact-cttaaccatgt-tgatgttgccattca--gGGATCTCTATGCTACTTACATCGTGGAGGGCTTGAGGAGGTAGACTTGTGCCGCTTCCTGGACCGAGAGGATGGATGTTGACGAAAATTGTGGAGAT-ATT-
















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|37377074|gb|CF625109.1|CF625109
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|32845833|gb|CD985514.1|CD985514
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|60345089|gb|DN212062.1|DN212062
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|78116468|gb|DV534855.1|DV534855
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTTTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|71761130|gb|DR959067.1|DR959067
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|211164202|gb|FL365728.1|FL365728
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCG
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCG
EST: gi|60400610|gb|DN233417.1|DN233417
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|60352136|gb|DN219109.1|DN219109
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|20301303|gb|BQ164246.1|BQ164246
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|33104183|gb|CF064143.1|CF064143
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|60393905|gb|DN226775.1|DN226775
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|21760122|gb|BQ635663.1|BQ635663
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGCAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|60394081|gb|DN226951.1|DN226951
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|60396637|gb|DN229505.1|DN229505
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|6973370|gb|AW438064.1|AW438064
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|60400269|gb|DN233076.1|DN233076
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|31405950|gb|CD484682.1|CD484682
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGAAATCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|19822092|gb|BQ048116.1|BQ048116
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|76287731|gb|DV027299.1|DV027299
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTTTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|6827019|gb|AW330662.1|AW330662
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTG
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTG
EST: gi|60395705|gb|DN228575.1|DN228575
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|71445655|gb|DR826705.1|DR826705
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|71758865|gb|DR956802.1|DR956802
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|76923128|gb|DV169344.1|DV169344
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|37397100|gb|CF635845.1|CF635845
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|60401073|gb|DN233880.1|DN233880
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|71444626|gb|DR825676.1|DR825676
EST:     AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTTTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|60342157|gb|DN209130.1|DN209130
EST:     AACGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGATCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA
EST: gi|91870562|gb|EB400946.1|EB400946
EST:     AATGACTTTTTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTAT                         GGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTTTGA
genomic: AATGACTTTCTACCAGCGAGCGCCGCTTATGAAGCCATACAGCACTCTATgtaagttgat ... ccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtttcgaccttcaagctaaccgcccagcaatgtgttgttcttccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGATGGCTAGGAAAGGTGGGGAGGATGTTGACGAAAAACTGGGAGACCATTT
                agctaac  putative branch site (score: 2)
                                     ttgttcttccatcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgatttatcgcaactgtgtcatctcaacacgtatcctcgtttcgaccttcaagctaaccgcccagcaatgtgttgttcttccatccacagGGACCTGTATGCTACATACATCGTTGAGGGCCTGAGGAGGTAGGATTCTGATGGCTAGGAAAGGTGGGGAGGATGTTGACGAAAAACTGGGAGACCATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG