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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtagagaaacaatatactgtgaactcttttgtgcaatgctgatgctctagcgttccatgtgttttatgtgttctaacaatagccaatttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTTCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAG

Basic information

species Oryza sativa
transcript LOC_Os06g49430.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G306028_T02 (Zea mays), 3'ss of exon 4
cttgtagagaaacaatatactgtgaactcttttgtgcaatgctgatgctctagcgttcc-atgt----gttttatgtgttctaacaatagccaatttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTTCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAG
  ||  || ||   |  |   || || | ||||  |  | | | ||| |  |   | |  ||||    | | |     |||| ||       |||||  || ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| ||||||||||
--tgctgaaaactgaggt---gtaaagtttttttagacaagattatgttgcaaaatccttatgttaccgctatccaaattctgactcattttaatttatatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTTCTCACTGGAAGGCCACTATTTCCTGGGAAGAATGTTGTACACCAATTAG

upper sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 4
cttgtagagaaacaatatactgtgaactcttttgtgca---atgctgatgctctagc-gttccatgt----gttttatgtgttctaacaatagccaatttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTTCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAG
       || ||   | | |||  ||||    |||  |   | | | ||| || |   |    ||||    | | |  |  |||| |||       |||  ||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| ||||||||||
-------agtaatc-tgtgctgaaaactgaggtgtatagacaagattatgttccaaaagccttatgttacagctatccgaattctgacacgtttttattcacatgcagTACACTCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCTGAACTTCTCACTGGAAGGCCACTATTTCCTGGGAAGAATGTTGTACACCAATTAG
















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|29645354|gb|CB650361.1|CB650361
EST:     AACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCT
genomic: AACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTT-CTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCT
EST: gi|29664602|gb|CB660877.1|CB660877
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|33795692|gb|CF323716.1|CF323716
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAA-                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|58687543|gb|CK076230.1|CK076230
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|58652759|gb|CK041439.1|CK041439
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|58663889|gb|CK052575.1|CK052575
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|58693904|gb|CK082591.1|CK082591
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|58663177|gb|CK051863.1|CK051863
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|58668308|gb|CK056994.1|CK056994
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|66913253|gb|CX100101.1|CX100101
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTACAAA                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|58661035|gb|CK049715.1|CK049715
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATCTGGAGTATTGGGTGCATATTTGCTGAGCTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|29627483|gb|CB632494.1|CB632494
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAA-                         TACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT
EST: gi|58668784|gb|CK057470.1|CK057470
EST:     CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAA                         TACACTCCTGCAATTGATATTTGGAGTATCGGGTGCATATTTGCTGAACTT
genomic: CAACGAGGTGGTACCGAGCACCTGAATTATGTGGCTCATTTTTCTCCAAAgtaaggtctt ... ttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctagcgttccatgtgttttatgtgttctaacaatagccaatttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTTCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAG
                            ttctaac  putative branch site (score: 1)
                 tgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtagagaaacaatatactgtgaactcttttgtgcaatgctgatgctctagcgttccatgtgttttatgtgttctaacaatagccaatttgcatacagTACACTCCTGCAATTGATATTTGGAGTATTGGGTGCATATTTGCTGAACTTCTCACTGGGAGACCACTATTTCCTGGGAAGAATGTTGTGCACCAATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA