RetrogeneDB ID: retro_cpor_1094

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_452:67704..68920(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH1
• Ensembl ID: ENSCPOG00000001485
• Aliases: None
• Description: None

Sequence

>retro_cpor_1094
ATGATGCTGGGCACCGAAGTTGGAGAGGAGTTCGTGGTGAAGATGCAGGGTTTGCCTTGGTCCTGCTCGGCTGATGAGGT
GCAGCGGTTCTTCTCCGCCTGCAAAATTCAAAATGGTGCTCAAGGTATTTGTTTCATCTACACCAGAGAAGGCAGACCGA
GTGGCGAGGCTTTTGTTGAACTTGAATCAGAAGATGAAGTCAAACTGGCCCTGAAAAAAGACAGAGAATCTATGGGACAC
AGATATGTTGAAGTATTCAAGTCAAACAACGTTGAAATGGATTGGGTGTTGAAGCATACTGGTCCAAATAGTCCTGACAC
GGCCAATGATGGCTTTGTACAGCTTAGAGGACTCCCCTTTGGATGTAGCAAGGAAGACATTGTTCAGTTCTTCTCAGGGT
TGGAAATCATGCCAAATGGGATAACATTGCCAGTGGACTTCCAGGGGAGGAGTATGGGGGAGGCCTTCGTGCAGTTTTTC
ACAGGAAATAGCTGAAAAGGCTCTAAAGAAACACAAGGAAAGAATAGAGCACAGGTATATTGAGATCTTTAAGGAGCAGT
CGGGCTGAAGTTAGAACTCACTATGACCCACCACGAAAGCTTATGGCCATGCAGCAGCCAGGCCCCTATGACAGACCTGG
GGCCGGCAGAGGGTATAACAGCATTGGCAGAGGAGCTGGCTTTGAGAGGATGAGGCATGGTGCCTACGGTGGAGGCTATG
ATGATTACAATGGCTATAATGATGGCTATGGATTTGGGTCAGATAGATTTGGAAGACCCTCAATTACTGTTTTTCAGGAA
TGTCTGATCACAGATATGGGGATGGTGGCTTTACTTTCCAGAGCACAACTGGACATTGTGTGCACATGCGGGGATTACTG
TACTGAGCTACCGAGAATGACATTTATAATTTCTTTTCACTGCTCAACCCTGTGAGAGTACACATTGAGATAGGTCCTGA
TGGGAGAGTTACTGGGGAAGCAGATGTTGAATTTGCAACTCATGAAGACGCTGTTGAAGCCATGTCAAAAGACAAAGCAA
ATATGCAACACAGATATGTAGAACTCTTCTTGAATTCTACAGCAGGAGCAAGCGGTGGTGCTTATTGTAGCCAAATGATG
GGAGGCATGGGCTTGTCAAACCAGTCCAGTTATGGTGGCCCGGCCAGCCAGCAGCTGAGCGGTGGCTATGGACGCGGCTA
CGGTGGCCAGAGCAGC

Alignment

ORF - retro_cpor_1094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 91.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MMLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
          MMLGTE.GE.FVVK..GLPWSCSADEVQRFFS.CKIQNGAQGI.FIYTREGRPSGEAFVELESEDEVKLA
Retrocopy MMLGTEVGEEFVVKMQGLPWSCSADEVQRFFSACKIQNGAQGICFIYTREGRPSGEAFVELESEDEVKLA

Parental  LKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
          LKKDRE.MGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFV.LRGLPFGCSKE.IVQFFSGLEI.PNG
Retrocopy LKKDRESMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVQLRGLPFGCSKEDIVQFFSGLEIMPNG

Parental  ITLPVDFQ-GRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK-SSRAEVRTHYDPPRKLMAMQRPG
          ITLPVDFQ.G...G.....F.SQEIAEKALKKHKERI.HRYIEIFK.SSRAEVRTHYDPPRKLMAMQ.PG
Retrocopy ITLPVDFQ>GGVWGRPSCSF-SQEIAEKALKKHKERIEHRYIEIFK>SSRAEVRTHYDPPRKLMAMQQPG

Parental  PYDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRD-LNYCFSGMSDHRYG
          PYDRPGAGRGYNSIGRGAGFERMR.GAYG...GGYDDYNGYNDGYGFGSDRFGR..LNYCFSGMSDHRYG
Retrocopy PYDRPGAGRGYNSIGRGAGFERMRHGAYG---GGYDDYNGYNDGYGFGSDRFGRP<LNYCFSGMSDHRYG

Parental  DGGSTFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSK
          DGG.TFQSTTGHCVHMRGL.Y.ATENDIYNFFS.LNPVRVHIEIGPDGRVTGEADVEFATHEDAV.AMSK
Retrocopy DGGFTFQSTTGHCVHMRGLLY*ATENDIYNFFSLLNPVRVHIEIGPDGRVTGEADVEFATHEDAVEAMSK

Parental  DKANMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPAS
          DKANMQHRYVELFLNSTAGASGGAY..........S.....GG....Q..GG.G......YGG..S
Retrocopy DKANMQHRYVELFLNSTAGASGGAYCSQMMGGMGLSNQSSYGGPASQQLSGGYG----RGYGGQSS

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
SRP017611_brain	0.46 RPM	141.49 RPM
SRP017611_kidney	0.94 RPM	229.06 RPM
SRP017611_liver	0.17 RPM	90.23 RPM
SRP040447_lung	0.05 RPM	338.31 RPM
SRP040447_skeletal_muscle	0.05 RPM	85.65 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1094 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1094 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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,