RetrogeneDB ID: retro_ogar_498

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873522.1:44553637..44554558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH1
• Ensembl ID: ENSOGAG00000012631
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H1 (H) [Source:HGNC Symbol;Acc:5041]

Sequence

>retro_ogar_498
ATGGTGAGCACCGAGGGTGGAGAGGGATTTGTGGTGAAGGTCTGGGGCTTGCCCTGGTCTTGCCCGGCTGAAGAAGGGCA
GCAGGTTTTTTTTGGCTGCAAAATTCAAAATTGGGCTCAAGGTATTCGTTTCATCCACACGACAGAAGGCAGAACGGAGT
GGTGAGGCTTTTGTTGAACTCAAATCAGAAAGTGAAGTCAAATTGGCCCAGAGAAAAGACAGAGAAACTATGGGACACAA
ATATGTTGAAGTGTTCAAGTCAAACAATGTTGAACTAGACTGGGTGTTGAAGCATACTGGTCCAAATAGTCCTGACATGG
CCAGTGATGGCTTTGTGCGGCTTAGAGGACTCGCCCATGAATGTAACAAGGAAGAAAGTGTTCATTTCTTCTCAGGGTTG
GAAATTGTGCCACATGGGGTAACATTGCCACTGGACTTCAGGGGAGGAGTACGGGGAAGGCCTTCGTACAGTTAGTTTCA
CAGGAAATTGCTGAAAAGCCTCAGAAGAAATACAAGGAAGGAATAGGGCACAGGTATATTGAAATCTTTAAGAGCAGTTG
AGCTGGTGTGAGAACTCACCATGATCCACCATGAAAGCTTACAGCCATGCATTCACCAGGTCCCTATGATAGACCTGGGG
CCGGCAGAGGGTATAACTGCATTGACAGAGGAGCCAACTTTGAGAGGATGAGGCGTGGTGCTTATGGTGGATGCTATAAT
GATTAGAATGGCTATAATGATAGCTATGTATTTGGGTCAGATAGATTTAGAAGAAATCTCAGTTACTGTTTTTTAGGAAT
GTCTGATCACTGATGTGGGGATGGTGGCTCTACTTTCCAGAGCACAACAGGACATTGTGTACACATGCATGGATTACCTT
ACAGAGCTATTGATAATGACATTTATAACTTTTTTCACCCT

Alignment

ORF - retro_ogar_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 65.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLGTEGGEGFVVKVRGLPWSCSAEEVQRFFSDCKIQNGAQGIRFIYTREGRP-SGEAFVELESEDEVKLA
          M..TEGGEGFVVKV.GLPWSC.AEE.Q.....CKIQN.AQGIRFI.T.EGR..SGEAFVEL.SE.EVKLA
Retrocopy MVSTEGGEGFVVKVWGLPWSCPAEEGQQXXXGCKIQNWAQGIRFIHTTEGRT>SGEAFVELKSESEVKLA

Parental  LKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
          ..KDRETMGH.YVEVFKSNNVE.DWVLKHTGPNSPD.A.DGFVRLRGL...C.KEE.V.FFSGLEIVP.G
Retrocopy QRKDRETMGHKYVEVFKSNNVELDWVLKHTGPNSPDMASDGFVRLRGLAHECNKEESVHFFSGLEIVPHG

Parental  ITLPVDF-QGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGP
          .TLP.DF.QGRSTG.AFVQ..SQEIAEK..KK.KE.IGHRYIEIFKSS.A.VRTH.DPP.KL.AM..PGP
Retrocopy VTLPLDF<QGRSTGKAFVQLVSQEIAEKPQKKYKEGIGHRYIEIFKSS*AGVRTHHDPP*KLTAMHSPGP

Parental  YDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDG
          YDRPGAGRGYN.I.RGA.FERMRRGAYGG.Y....D.NGYND.Y.FGSDRF.R.L.YCF.GMSDH..GDG
Retrocopy YDRPGAGRGYNCIDRGANFERMRRGAYGGCY---ND*NGYNDSYVFGSDRFRRNLSYCFLGMSDH*CGDG

Parental  GSTFQSTTGHCVHMRGLPYRATENDIYNFFSP
          GSTFQSTTGHCVHM.GLPYRA..NDIYNFF.P
Retrocopy GSTFQSTTGHCVHMHGLPYRAIDNDIYNFFHP

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_498 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 22 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008888	2 retrocopies	retro_amel_57, retro_amel_9,
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Choloepus hoffmanni	ENSCHOG00000003841	4 retrocopies	retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus	ENSCJAG00000009931	1 retrocopy	retro_cjac_127,
Cavia porcellus	ENSCPOG00000001485	5 retrocopies	retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Felis catus	ENSFCAG00000001204	2 retrocopies	retro_fcat_131, retro_fcat_27,
Homo sapiens	ENSG00000169045	2 retrocopies	retro_hsap_3322, retro_hsap_4911,
Myotis lucifugus	ENSMLUG00000016625	1 retrocopy	retro_mluc_124,
Macaca mulatta	ENSMMUG00000010843	1 retrocopy	retro_mmul_2,
Monodelphis domestica	ENSMODG00000009436	3 retrocopies	retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Otolemur garnettii	ENSOGAG00000012631	2 retrocopies	retro_ogar_208, retro_ogar_498 ,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pongo abelii	ENSPPYG00000016121	1 retrocopy	retro_pabe_110,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Rattus norvegicus	ENSRNOG00000003399	1 retrocopy	retro_rnor_340,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,
Sus scrofa	ENSSSCG00000014022	1 retrocopy	retro_sscr_70,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,