RetrogeneDB ID: retro_ogar_3087

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873711.1:2816702..2817816(-)
• Located in intron of: ENSOGAG00000028267

Retrocopy information

• Ensembl ID: ENSOGAG00000002598
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARPC1B
• Ensembl ID: ENSOGAG00000010872
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1B, 41kDa [Source:HGNC Symbol;Acc:704]

Sequence

>retro_ogar_3087
ATGGCCTACCACAGCTTCCTGGTGGAGCCCATCAGCTGCCATGCCTGGAACAAGGACCGCACCCAAATTGCCATCTGCCC
AAACAACCATGAGGTGCACATCTATGAGAAGAGTGGGACCAAGTGGACCAAGGTGCATGAGCTCAAGGAGCACAATGGGC
AGGTGACAGGCATCGACTGGGCTCCTGAGAGTAACCTCATTGTAAGCTGCGGCACAGATCGCAACACCTACGTGTGGACA
CTGAAGGGCCGCACATGGAAGCCTACCCTGGTCATCCTGTGGATTAACCGGGCTGCTCACTGTGTGCGCTGGGCCCCCAA
CGAGAACAAATTTCCTGTGGGCAGTGGCTCCCGTGTTATCTCCATCTGTTATTTTGAGCAGGAGAATGACTGGTGGGTGT
GCAAGCACATCAAAAAGCCCTCCGCTCCACTGTTCTCAGCGTGGACTGGGACCCCAACAACATGCTCCTGGCTGCAGGCT
CCTGTGACTTCAAGTGCTGGATCTTCTCAGCTTACATCAAGGAGGTGGAGGAGAGGCCGGCACCCACACCATGGGGCTCC
AAGATGTCCTTTGGTGAGCTGATGTTTGAATCCAGCAGTAGCTGTGGCTGGGTGCATGGCGTTTGCTTCTCAGTCAGCGG
GAGCCGTGTGGCCTGCGTCAGTCATGACAGCACTGTGTGCCTGGCTGATGCTGACAAGAAGATGGCCGTTGCAACCCTGG
CCTCTGAAACTCTGCCGCTGCTGGCACTGACCTTCATCACAGAAAACAGCCTGGTGGCAGCGGGCCACGACTGCTTCCCA
GTGCTCTTTACCTATGATGGCACAGCAGGGACGCTGAGCTTCAGCGGGAGGCTGGACGTGCCCAAGCAGAGCTGCAGCGG
GGCTTGACAGCCCATGAATGCTTCCAGAACCTAGACAAGAAAGCGAGCTCGGAGGGTGGCCCGTCCTCAGGGGCTGGCCT
TGACTCACTGCACAAGAACAGCGTCAGCCAGATCTCGGTGCTCAGTGGGGGCAAGGCCAAGTGCTCACAATTTTCCACCA
CTGGCATGGATGGTGGTATGAGCATCTGGGACGTGAAGAGCTTGGAGTCAGCATTGAAAGACCTCAAGATCAAA

Alignment

ORF - retro_ogar_3087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGTKWTKVHELKEHNGQVTGIDWAPESNRIVTC
          MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGTKWTKVHELKEHNGQVTGIDWAPESN.IV.C
Retrocopy MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGTKWTKVHELKEHNGQVTGIDWAPESNLIVSC

Parental  GTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNENKFAVGSGSRVISICYFEQENDWWVCKHIKKP
          GTDRN.YVWTLKGRTWKPTLVIL.INRAA.CVRWAPNENKF.VGSGSRVISICYFEQENDWWVCKHIKKP
Retrocopy GTDRNTYVWTLKGRTWKPTLVILWINRAAHCVRWAPNENKFPVGSGSRVISICYFEQENDWWVCKHIKKP

Parental  -IRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVC
          ..RSTVLS.DW.PNN.LLAAGSCDFKC.IFSAYIKEVEERPAPTPWGSKM.FGELMFESSSSCGWVHGVC
Retrocopy <LRSTVLSVDWDPNNMLLAAGSCDFKCWIFSAYIKEVEERPAPTPWGSKMSFGELMFESSSSCGWVHGVC

Parental  FSASGSRVAWVSHDSTVCLADADKKMAVATLASETLPLLALTFITENSLVAAGHDCFPVLFTYDGIAGTL
          FS.SGSRVA.VSHDSTVCLADADKKMAVATLASETLPLLALTFITENSLVAAGHDCFPVLFTYDG.AGTL
Retrocopy FSVSGSRVACVSHDSTVCLADADKKMAVATLASETLPLLALTFITENSLVAAGHDCFPVLFTYDGTAGTL

Parental  SFGGRLDVPKQSS-QRGLTARERFQNLDKKASSEGGASSGAGLDSLHKNSVSQISVLSGGKAKCSQFCTT
          SF.GRLDVPKQS..QRGLTA.E.FQNLDKKASSEGG.SSGAGLDSLHKNSVSQISVLSGGKAKCSQF.TT
Retrocopy SFSGRLDVPKQSC<QRGLTAHECFQNLDKKASSEGGPSSGAGLDSLHKNSVSQISVLSGGKAKCSQFSTT

Parental  GMDGGMSIWDVKSLESALKDLKIK
          GMDGGMSIWDVKSLESALKDLKIK
Retrocopy GMDGGMSIWDVKSLESALKDLKIK

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_3087 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046248	2 retrocopies	retro_btau_1547, retro_btau_473,
Canis familiaris	ENSCAFG00000015081	1 retrocopy	retro_cfam_1568,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365,
Echinops telfairi	ENSETEG00000009924	2 retrocopies	retro_etel_1076, retro_etel_1275,
Gorilla gorilla	ENSGGOG00000013186	2 retrocopies	retro_ggor_1337, retro_ggor_1455,
Microcebus murinus	ENSMICG00000017424	1 retrocopy	retro_mmur_602,
Myotis lucifugus	ENSMLUG00000010933	1 retrocopy	retro_mluc_974,
Mustela putorius furo	ENSMPUG00000016522	1 retrocopy	retro_mputfur_1578,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340, retro_mmus_3623,
Otolemur garnettii	ENSOGAG00000010870	6 retrocopies	retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Otolemur garnettii	ENSOGAG00000010872	2 retrocopies	retro_ogar_2380, retro_ogar_3087 ,
Rattus norvegicus	ENSRNOG00000000991	2 retrocopies	retro_rnor_1105, retro_rnor_967,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,