RetrogeneDB ID: retro_cpor_937

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_35:12081457..12082723(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000005595
• Aliases: None
• Description: None

Sequence

>retro_cpor_937
GACAGGGATGATCCTTCTTCTGAGCAAGATAGAAATTGAGATTCTGACAAAACAGACACAGACTGGAGGGCCCATCTTGC
CACAGACAGCTTTGATGACTACCTACCAAAAAGAGGTGATGATAGTTTTCGAGACAAGTTTTGAAATAATTATGATTCAG
ACTGATACCGTGATGGGTATGGGGATTGGGATGGCTATCATGGTGGCCCACGCTGGCATATAGGTCAATATGGAGGCCAA
GACTGATATGCTGATGAGGCAGCAGAGACTATGATAGAGGCTATGATTCCATAATTGACAGTGGCAGAAAAACCTTTGGT
GGTGGGCACCATAGAGATGATGATTACAGAAGAGCAAGAAACCGGTATGACAGATGAGATGATCGACCCTGTAGCTCCAG
AGATGATTAACACAGGACAGTTATAGGTGTGATGATAGAGATCCCCACCAAAGACCCAGGCTGAACCTAAAGCCTTGGAG
TACTCCTAAGGAACATGATTCTTCTGCTGGCACCTCCCACTCCAGTCAAGAAGTTGCTATCTCTGTAGGGGCAAAGCCTG
TTGACACGGCTGCCAGAAAAAGAGAAGTAGAAGAATGGCTGCAAAAGGAGCAGGATAAACTGCAGCATCAGCTGGATGAG
CAGAAGTTGGAATGGCGGTCTCAGAAGAGACGCCCAAGCTGGCAAAGTGAAGAAACTCAGAAAAGGGAAAGATGAAGCAC
AGAAAGCGAATCCTCACAGACTGGGACCTCAGCCCCGTTTGGCAGAAATGCTTGAAGAAGAGACAGCAAGAAGTTTCTAG
AAAATGAAACACTCAATAAGGAGGAAGATTGTCACTTTCCAACTAGTAAGCGTTCCAAACCTAATTAGCCTCTAAAAGTA
ATGTCAGCTCCTCCACCGAAGGAGAATGCATGGATGAAGGGAAGTTCTAACCCTCCTGTTGAATCTCAGAGCTCACACAG
AGCACCTGGAGGGGGGGAATCTAGCTCCAGCTCAGCCTGCCAAGTAGAGACCAGCAAGGAAAGATGAAAATAATCAGATG
AGTACCCAAAAGGCCAAACTGGGAACTCCATCCGTAGTTCAGGAGATGGACGGAACAAAGACCATTGGAAGGAGTCGAAT
AGGAAAGATGGGAAAAAGGATCAGGACTCTAGATCCAACCTGAGCCAAAGAAACTTGAGGAAAATCCAGTCTCCAAGTTC
AGTTCTGCAAGCAAGTATGCTGCTCTCTGAATGGGTGGTGAAGATGAAAATGAAGACTACACTGAA

Alignment

ORF - retro_cpor_937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.59 %
• Parental protein coverage: 71.08 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDYPPRRGDDSFGDKYRDRYDSDRYRDGYRDRDGYRDGP
          DRDD.S...DRN.DSDKTDTDWRA..ATDSFDDY.P.RGDDSF.DK....YDSD.YRDGY.D.DGY..GP
Retrocopy DRDDPSSEQDRN*DSDKTDTDWRAHLATDSFDDYLPKRGDDSFRDKF*NNYDSD*YRDGYGDWDGYHGGP

Parental  RRDMDRYGGRDRYDDR-GSRDYDRGYDSRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDDRPWGSRD
          R.....YGG.D.Y.D..GSRDYDRGYDS.I.SGR..FG.G..RDDDYR....R...RYDR.DDRP..SRD
Retrocopy RWHIGQYGGQD*YADE<GSRDYDRGYDSIIDSGRKTFGGGHHRDDDYR----RARNRYDR*DDRPCSSRD

Parental  D-YSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSSRAASIFGGAKPVDTAAREREVEERLQKE
          D....D.YR.DDR.P.QRP.LNLKP.STPKE.DSSA.TS.SS....I..GAKPVDTAAR.REVEE.LQKE
Retrocopy D<LTQDSYRCDDRDPHQRPRLNLKPWSTPKEHDSSAGTSHSSQEVAISVGAKPVDTAARKREVEEWLQKE

Parental  QEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRTGSESSQTGTSAPSGRNARRRESEKSLENETLSK
          Q.KLQ.QLDE.KLE.R...R.PSW.SEETQ.RER..T.SESSQTGTSAP.GRNA.RR.S.K.LENETL.K
Retrocopy QDKLQHQLDEQKLEWRSQKRRPSWQSEETQKRER*STESESSQTGTSAPFGRNA*RRDSKKFLENETLNK

Parental  EEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPSARSQSSDTEHQSPTSGGGK-LAPAQPSEEGP
          EEDCH.PTSK..KP..PLKVM.APPPKENAW.K.SSNP...SQSS...H..P..GGG..LAPAQP....P
Retrocopy EEDCHFPTSKRSKPN*PLKVMSAPPPKENAWMKGSSNPPVESQSS---HRAP--GGGE>LAPAQPAK*RP

Parental  ARKADENNGMSTQ-KGQTGNSIRGLGDGGNKDHWKESDRKDGKKDQDSRS-APEPKKLEENPASKFSSAS
          ARK.DENN.MSTQ.KGQTGNSIR..GDG.NKDHWKES.RKDGKKDQDSRS..PEPKKLEENP.SKFSSAS
Retrocopy ARK-DENNQMSTQ<KGQTGNSIRSSGDGRNKDHWKESNRKDGKKDQDSRS<QPEPKKLEENPVSKFSSAS

Parental  KYAALCMDGEDDNEGEDYTE
          KYAAL.M.GED.N..EDYTE
Retrocopy KYAAL*MGGEDEN--EDYTE

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	0.00 RPM	70.40 RPM
SRP017611_kidney	0.00 RPM	93.38 RPM
SRP017611_liver	0.00 RPM	90.88 RPM
SRP040447_lung	0.00 RPM	98.49 RPM
SRP040447_skeletal_muscle	0.00 RPM	104.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_937 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_937 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 17 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937 ,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,