RetrogeneDB ID: retro_ogar_1463

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873548.1:13045521..13046286(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SLBP
• Ensembl ID: ENSOGAG00000009750
• Aliases: None
• Description: stem-loop binding protein [Source:HGNC Symbol;Acc:10904]

Sequence

>retro_ogar_1463
ATGGCCTGTCGGCCGCGAAACCCGTCCAAACACCGAGCCGCTGTGACAGGGACGCGAGCCCGCCGTCCCCGGCAAGATGG
AGCCTCGGACCGAAGCGCAGAGCCGACAGGAGGCGCAGGAAGCCCGAGGACGCCCAGCAGGAGGAGCGCCGGGCCGCCCA
CCGCAGGCCCGAGAGCTTTACCACTCCCGAAGGTCCCAAGCCCCGTTCTAGATGTTCAGACAGGGCAAGTGCAGCTGAGG
AAGATGAGATGAGGACCAGAGTTAACAAGGAAATAGCAAGATATAAAAGAAAACTTCTCATAAATGAATTTGGAACAGAG
AGAACATCATCATCAGGAAGTTCTGATTCAAAGGAGTCTATGTCTACTGTCCCAGCTGATTTTGAGACAGACGAAAGTGT
CCTGATGAGGAGACAGAAACAGATCAACTATGGAAAGAACACAATTGCCTATGACCGCTATATTAAAGAAGTCCCAAGAC
ACCTTTGGCAACCCGGCATCCATTCCAAGACGCCCAACAAGTTTAAGAAGTATAGTCACCGGTCGCGGGACCAGCAGATA
AGACTCTGGAAGGTGGCACTGCATTTTTGGGATCCTCCAACTGAAGAAGGATGTGATTTGCAGGAAATACACCCTGTAGT
CCTGGAATCCCCAGAAGTGGCTCTGAGCCTCAGATGAGCTCTCAGGATGACTTCCATGTCTACCTGGCACACTCACCAAG
GTCAGACGCGTGGACTGCCAAGTGGAGGACGAGTTTGACTTGGAA

Alignment

ORF - retro_ogar_1463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.42 %
• Parental protein coverage: 94.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASRPRSPSKYG-SRCDGDASPPSPARWSLGRKRRADGRRRKPEDAEQDECRAADRRPESFTTPEGPKPR
          MA.RPR.PSK...SRCD.DASPPSPARWSLG.KRRAD.RRRKPEDA.Q.E.RAA.RRPESFTTPEGPKPR
Retrocopy MACRPRNPSKHR<SRCDRDASPPSPARWSLGPKRRADRRRRKPEDAQQEERRAAHRRPESFTTPEGPKPR

Parental  SRCSDWASAVEEDEMRTRVNKEMARYKRKLLINEFGRERKSSSGSSDSKESMSTVPADFETDESVLMRRQ
          SRCSD.ASA.EEDEMRTRVNKE.ARYKRKLLINEFG.ER.SSSGSSDSKESMSTVPADFETDESVLMRRQ
Retrocopy SRCSDRASAAEEDEMRTRVNKEIARYKRKLLINEFGTERTSSSGSSDSKESMSTVPADFETDESVLMRRQ

Parental  KQINYGKNTIAYDRYIKEVPRHLRQPGIHPKTPNKFKKYSRRSWDQQIRLWKVALHFWDPPAEEGCDLQE
          KQINYGKNTIAYDRYIKEVPRHL.QPGIH.KTPNKFKKYS.RS.DQQIRLWKVALHFWDPP.EEGCDLQE
Retrocopy KQINYGKNTIAYDRYIKEVPRHLWQPGIHSKTPNKFKKYSHRSRDQQIRLWKVALHFWDPPTEEGCDLQE

Parental  IHPIDLESPE-SGSEPQMSSQDDFDVY-SGTPTKVRHVDCQVEDEFDLE
          IHP..LESPE.SGSEPQMSSQDDF.VY..GT.TKVR.VDCQVEDEFDLE
Retrocopy IHPVVLESPE<SGSEPQMSSQDDFHVY<PGTLTKVRRVDCQVEDEFDLE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1463 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001328	1 retrocopy	retro_btau_1456,
Cavia porcellus	ENSCPOG00000000031	1 retrocopy	retro_cpor_364,
Mus musculus	ENSMUSG00000004642	1 retrocopy	retro_mmus_1169,
Otolemur garnettii	ENSOGAG00000009750	1 retrocopy	retro_ogar_1463 ,
Pteropus vampyrus	ENSPVAG00000002807	2 retrocopies	retro_pvam_490, retro_pvam_941,
Rattus norvegicus	ENSRNOG00000037162	2 retrocopies	retro_rnor_1864, retro_rnor_2016,
Tarsius syrichta	ENSTSYG00000000376	2 retrocopies	retro_tsyr_1595, retro_tsyr_482,
Tursiops truncatus	ENSTTRG00000010901	1 retrocopy	retro_ttru_10,