RetrogeneDB ID: retro_ogar_1378

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873544.1:8305642..8306337(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF1
• Ensembl ID: ENSOGAG00000026029
• Aliases: None
• Description: activating transcription factor 1 [Source:HGNC Symbol;Acc:783]

Sequence

>retro_ogar_1378
CCTCCACCTGGGTCGGCAGTTCAGGGAGCCATCTTTCTCATATTGCTCGCCAGGCAGCATCTTATCAGAAAGTGGGCAGT
CCCAGGCCTCATCTGACAGCACAGGCTCCTCGCAGAAAGCCCACAGGATCCTCGCATGGTGTCCACCTTACAGAATAACT
TGGAAAGACCTATCTTCTGAAGATGCAAGGAGCAGAAAAGGAGACAGAGAAAACCCTGGAGTTTCTGCTGTCACTTCTAT
GTCGGTTCCGACTCCCATCCGTCAGACTAGCAGCCGACAGTACATTGCCATTGCCCCAAATGGAGCCTTACAGTTGGCCA
GTCCGGGCCCAGATGGAGTACAGGGGCCTCAGACCTTAACCATGGCAAGTTCGGGCAGTACTCAGCAAGGTACAGCTGTT
CTCCAGGATGCACAGCAAATACTTGTGCCCAGCAATCTAGTGACAGTATTGACTACATCGGTAGACACGCAAGCATATCA
GATTCATACCACACCCTCAGATACTTCTCTACCACAAATTGTGGTGATGACATCCTGTGACTCTTACATCTCAGACAACT
AACATGGATGACCCCCAACTGAAAAGAGAAACAAGGTTAATGAAAAACAGAGAAGCTGCTCGAGAATGTCGCAGAAAGAA
GAAATAGTATATGAAATGTTTGGAAACTCAAGTTGCCATCCTGGAAAATCAACAT

Alignment

ORF - retro_ogar_1378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.95 %
• Parental protein coverage: 78.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PQPGSAVQG-THLSHIAQQVSS-LSESEESQDSSDSIGPSQKAHGILARRPSYRKIFKDLSSEDTRSRKG
          P.PGSAVQG..HLSHIA.Q..S.LSES..SQ.SSDS.G.SQKAH.ILA..P.YR...KDLSSED.RSRKG
Retrocopy PPPGSAVQG<SHLSHIARQAAS<LSESGQSQASSDSTGSSQKAHRILAWCPPYRITWKDLSSEDARSRKG

Parental  DGENSGVSAVTSMSVPTPIYQTSSGQYIAIAPNGALQLANPGTDGVQGLQTLTMTNSGNTQQGTTILQYA
          D.EN.GVSAVTSMSVPTPI.QTSS.QYIAIAPNGALQLA.PG.DGVQG.Q..T.T.......G.T....A
Retrocopy DRENPGVSAVTSMSVPTPIRQTSSRQYIAIAPNGALQLASPGPDGVQGPQ--TLTMASS---GSTQQGTA

Parental  QTSDGQQILVPSNQVVVQTASGDMQTYQIRTTPSATSLPQTVVMTS-PVTLTSQTTKTDDPQLKREIRLM
          ...D.QQILVPSN.V.V.T.S.D.Q.YQI.TTPS.TSLPQ..V....PVTLTSQTT..DDPQLKRE.RLM
Retrocopy VLQDAQQILVPSNLVTVLTTSVDTQAYQIHTTPSDTSLPQ-IVVMT>PVTLTSQTTNMDDPQLKRETRLM

Parental  KNREAARECRRKKKEYVKCLENRVAVLENQN
          KNREAARECRRKKK.Y.KCLE..VA.LENQ.
Retrocopy KNREAARECRRKKK*YMKCLETQVAILENQH

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_1378 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008000	2 retrocopies	retro_eeur_332, retro_eeur_704,
Homo sapiens	ENSG00000123268	1 retrocopy	retro_hsap_3633,
Oryctolagus cuniculus	ENSOCUG00000017023	1 retrocopy	retro_ocun_383,
Otolemur garnettii	ENSOGAG00000026029	1 retrocopy	retro_ogar_1378 ,
Procavia capensis	ENSPCAG00000010038	2 retrocopies	retro_pcap_303, retro_pcap_442,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635,