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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccgagcttcgctgctcgatccagtgccaattttgatcttcgatctagtttgaactagacgagtcatgtgcttttccctctctgttgactcttgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTCTGCGCCTCCTGCTCTTATAG

Basic information

species Oryza sativa
transcript LOC_Os01g61580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61580.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G897342_T02 (Zea mays), 3'ss of exon 1
gtaagtccgagcttcgctgctcgatccagtgccaattttgatcttcgatcta---gtttgaactag-acgagtcatgtgcttttccctctctgttgactcttgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTCTGCGCCTCCTGCTCTTATAG
||  || | || | ||   |  | |   |||     |||| |   |||||||   ||  || ||    ||  || |||||||| |   | |  ||    |||    || ||||||| |||||||| ||  ||| |||||||||||||||||| || |||||||||||||||||||| || ||
gtttgtactag-tacgggccctggttgggtgg----tttggtgcccgatctaactgtccgagctgatgcggttcttgtgctttgcttccgccttttctcctt----tgcagGAGCCACAGGTGGACGGAACTGGCTCCGGCACCACCGTCGACTTCAAGTTCTGCGCCTCCTGCTCGTACAG
















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|86831226|gb|CI297495.1|CI297495
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         GAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|88447799|gb|CI576995.1|CI576995
EST:     TCCAGCCCGACGACATCGCCGC-GATGCCGCCGTTTCCGCGCAGATTGCT                         GAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|87023709|gb|CI286460.1|CI286460
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         GAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|117222253|gb|CT845768.1|CT845768
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         ---------GTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|4716086|gb|AU057202.1|AU057202
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         GAGCCGCA-GTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|88739798|gb|CI763306.1|CI763306
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         GAGCCGNAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|27577857|gb|CB000552.1|CB000552
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         GAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|88727221|gb|CI750876.1|CI750876
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         GAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|88739031|gb|CI762539.1|CI762539
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         GAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
EST: gi|14192082|gb|AU184293.1|AU184293
EST:     TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCT                         GAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC
genomic: TCCAGCCCGACGACATCGCCGCCGATGCCGCCGCTTCCGCGCAGATTGCTgtaagtccga ... tgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgaactagacgagtcatgtgcttttccctctctgttgactcttgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTCTGCGCCTCCTGCTCTTATAG
                                   tgttgac  putative branch site (score: 3)
                       cttttccctctctgtt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccgagcttcgctgctcgatccagtgccaattttgatcttcgatctagtttgaactagacgagtcatgtgcttttccctctctgttgactcttgtgttgtagGAGCCGCAGGTGGATGGGCCTGCCTCCGGCACCACCGTCGAGTTGAAGTTCTGCGCCTCCTGCTCTTATAG

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