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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccaatcccaggaaacgttctgatagcacagctcattgcttaccataattattgtacttgataccgtggtctgctaatcatttttttctgggtcgagtaatcaatttcgtttctacatctccctcttttcacccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTCTTAGAAGGATCAGGAAAAGCTGCTGAGATAGCAGACATCACCCTCAACA

Basic information

species Oryza sativa
transcript LOC_Os01g54020.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54020.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 14
---------------------gtattccaatc-ccaggaaacgttctgatagcacagctcattgcttaccataattattgtacttgataccgtggtctgctaatcatttttttctgggtcgagtaatcaatttcg-----------tttctacatctccctcttttc---acccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTCTTAGAAGGATCAGGAAAAGCTGCTGAGATAGCAGACATCACCCTCAACA
                       | |   ||     | || | || || |  | |   ||     |   |  ||  |||||| |||| |   |  | |    ||||  || || |   | |  ||   ||| ||            |||||  | ||   | |||||   |||  | ||||| || || |||||||||||||||||||| |  || ||||||  ||| || ||||||||| ||| |||||||||||||||||| ||||||||||| ||||
gttcaatgacccttgatctgtacagtttgataatttgtaacccttatgcttacccccatc-caattggactgaaccattgtatttgacaaatt--tttagcgatcaagttctttttatttgcatagctaatctccatacgaatccttttctttaactattttttttccacacctttgtagGTTCGTTATGAGGAGATAATGTCTGATCCAGCCTACTTGGATAATGTCCTTTTAGAAGGAGCAGTAAAAGCTGCTGAGATAGCGGACATCACCCTGAACA
















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|86833985|gb|CI340124.1|CI340124
EST:     CAAAACAACTCTTACAGATGCATTGATTGATCATCTGCAACCTATCCAG                         GCCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
genomic: CAAAACAACTCTTACAGATGCATTGATTGATCATCTGCAACCTATCCAGgtattccaat ... acccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
EST: gi|89168243|gb|CI109447.1|CI109447
EST:     TCAAAACGACTCTTACAGATGCCTTGATTGATCATCTGCAACCTATCCAG                         GTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
genomic: TCAAAACAACTCTTACAGATGCATTGATTGATCATCTGCAACCTATCCAGgtattccaat ... acccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
EST: gi|88270065|gb|CI381363.1|CI381363
EST:     TCATCTGCAACCTATCCAG                         GTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
genomic: TCATCTGCAACCTATCCAGgtattccaat ... acccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
EST: gi|88844589|gb|CI020436.1|CI020436
EST:     TCAAAACAACTCTTACAGATGCATTGATTGATCATCTGCAACCTATCCAG                         GTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
genomic: TCAAAACAACTCTTACAGATGCATTGATTGATCATCTGCAACCTATCCAGgtattccaat ... acccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
EST: gi|89177147|gb|CI043650.1|CI043650
EST:     TCTAAACAACTCTTACAGATGCATTGATTGATCATCTGCAACCTATCCAG                         GTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC
genomic: TCAAAACAACTCTTACAGATGCATTGATTGATCATCTGCAACCTATCCAGgtattccaat ... acccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgggtcgagtaatcaatttcgtttctacatctccctcttttcacccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTCTTAGAAGGATCAGGAAAAGCTGCTGAGATAGCAGACATCACCCTCAACA
                   tttcgtttctacatct  CT-rich tract
            taatcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattccaatcccaggaaacgttctgatagcacagctcattgcttaccataattattgtacttgataccgtggtctgctaatcatttttttctgggtcgagtaatcaatttcgtttctacatctccctcttttcacccgtctagGTCCGCTACGAGGAGATAATGTCTGATCCTGGTTATTTGGATGGTGTTCTCTTAGAAGGATCAGGAAAAGCTGCTGAGATAGCAGACATCACCCTCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT