RetrogeneDB ID: retro_ggor_1299

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:41361772..41362642(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH1
• Ensembl ID: ENSGGOG00000025844
• Aliases: None
• Description: None

Sequence

>retro_ggor_1299
ATGATGTTGGGCACCAAAGGTGGCGAGCGGTTTATGTTGAAGGTCCACGGCTTGCCCTGGTCTTGCTTGGCCGATGAAGT
GCAGCGTTTTTTTCTGACTGCAAAATTCAAAATAAGGCTCAAGGTATTCGTTTCATCTACAACAGAGAAGGCAGGCTGGG
TGACAAGGCTTTTGTTGAACTTGAATCAGAAGATGAAGTCAAATTGGCCCTGAAAAAGGACAGAGAAACTATGTGACACA
GTTTTGTTGAAGCATTCAAGTCAAACAACGTTGAAATGGATTGGGTGTTGAAGCATACCGGTCCAAATAGTCCTGACACG
GCCAGTGATGGCTTTGTACAGCTTAGAGGACTTCCCTTTGAATGCAGCAAAGAAGAAATTGTTCAGTTCTTCTCAGGGTT
GGAAATCGTACCAAATGGGATAACATTGCCAGTGGACTCCAGGGTGGGAGTACAGGGGAGGCCTTCGTGCAGTTTGCTTC
ACAGGAAATAACCAAAAAGGCTCTAAAGAAACACAAGGAAAGAATAGGGCACAGGTATATTGAAATCTTTAAGAGCAGCA
GGGCTGAAGTTAGAACTCACTACAATCCACCATAAAAGCTTATGGCCATGCAGCGGCCAGGTCCCATGACAGACCTGGTT
CTGGCAGAGGTTTTAACAGCATTGGCAGAGGAGCTGGCTTACAGAGGATGAGGCATGGTGCTTATGGTGGAGGATATGGA
GTCTATGACAATTATAATGGCTATGGCTATGGATTTGGGTCAGATAGATTTGGAAGAGACCTCAATTATTGTTTTTCAGG
AATGTCTGATCACAAATATGGGGATGGTGGCTCTACCTTCCAGAGCACAACAGGACACTGTATATACGTG

Alignment

ORF - retro_ggor_1299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.81 %
• Parental protein coverage: 64.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MMLGTEGGEGFVVKVRGLPWSCSADEVQRFF-SDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKL
          MMLGT.GGE.F..KV.GLPWSC.ADEVQRFF.SDCKIQN.AQGIRFIY.REGR....AFVELESEDEVKL
Retrocopy MMLGTKGGERFMLKVHGLPWSCLADEVQRFF<SDCKIQNKAQGIRFIYNREGRLGDKAFVELESEDEVKL

Parental  ALKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPN
          ALKKDRETM.H..VE.FKSNNVEMDWVLKHTGPNSPDTA.DGFV.LRGLPF.CSKEEIVQFFSGLEIVPN
Retrocopy ALKKDRETM*HSFVEAFKSNNVEMDWVLKHTGPNSPDTASDGFVQLRGLPFECSKEEIVQFFSGLEIVPN

Parental  GITLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPG
          GITLPVD..QG.STGEAFVQFASQEI..KALKKHKERIGHRYIEIFKSSRAEVRTHY.PP.KLMAMQRPG
Retrocopy GITLPVD<LQGGSTGEAFVQFASQEITKKALKKHKERIGHRYIEIFKSSRAEVRTHYNPP*KLMAMQRPG

Parental  P-YDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYG
          P..DRPG.GRG.NSIGRGAG..RMR.GAYGGGYG.YD.YNGY..GYGFGSDRFGRDLNYCFSGMSDH.YG
Retrocopy P<HDRPGSGRGFNSIGRGAGLQRMRHGAYGGGYGVYDNYNGY--GYGFGSDRFGRDLNYCFSGMSDHKYG

Parental  DGGSTFQSTTGHCVHM
          DGGSTFQSTTGHC...
Retrocopy DGGSTFQSTTGHCIYV

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	144.05 RPM
SRP007412_cerebellum	0.04 RPM	224.10 RPM
SRP007412_heart	0.00 RPM	78.89 RPM
SRP007412_kidney	0.00 RPM	227.75 RPM
SRP007412_liver	0.32 RPM	176.73 RPM
SRP007412_testis	0.73 RPM	349.44 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1299 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009389	1 retrocopy	retro_btau_130,
Canis familiaris	ENSCAFG00000000336	2 retrocopies	retro_cfam_200, retro_cfam_230,
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,
Dipodomys ordii	ENSDORG00000005453	1 retrocopy	retro_dord_3,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Gorilla gorilla	ENSGGOG00000025844	2 retrocopies	retro_ggor_1299 , retro_ggor_177,
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,
Mustela putorius furo	ENSMPUG00000000693	1 retrocopy	retro_mputfur_156,
Mus musculus	ENSMUSG00000007850	1 retrocopy	retro_mmus_142,
Nomascus leucogenys	ENSNLEG00000026658	3 retrocopies	retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,
Ictidomys tridecemlineatus	ENSSTOG00000016376	2 retrocopies	retro_itri_66, retro_itri_78,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,