RetrogeneDB ID: retro_cpor_264

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_11:48781171..48781794(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRPDL
• Ensembl ID: ENSCPOG00000015619
• Aliases: None
• Description: None

Sequence

>retro_cpor_264
GCCAGGGGGTCCACGATCAACTCAAGCAAGAACCAGTACAATGACTTTAAAATGTTTACTGGAGGCTTGAGCTGGAATAC
AGCAAGAAAGATCTGACTGAATATTTGTCTTGATTTGGGAAGTTGTAGACTGAACACTTAAGACAGATCCAGTCATGGAA
GATCAAGAGGATTTAGATTTGTACTTTTCAAAAGATGATGCTGGTGTTGATAAGGTTTTGGAACTAAAAGAACACAAACT
GGATGGCAAATTGATAGACCCCCAAAAGGCCAAAGCTTTAAAAGAGAAAGAACCTTCTAAAAAGGTGTTTGTGGGTGGAT
TGAGCCCAGATACTTCTGAAGAACAAATTAAAGAATATTTTGGAGCCTGTGGAGAGATCAAAAATATTGAACTTCCTGTG
GATACAAAAACAAATGAAGGGAAACGATTTTGCTTCATTACATATACACATGAAGAGCCATCAAGAATTTGTTAGAAAGC
AGATACCGTCACACTGGTTCTCGAAAGTGTGAAATCAAAGTTTTACAACCCAAAAAGGAGGAAGAGGTGCTGCAGCTGGG
GGACGAGGTGGTACGAGGGGTCGTGGCTAAGGTCAGGGCCAAAACTGGAACCCAGGATTTAAT

Alignment

ORF - retro_cpor_264 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.36 %
• Parental protein coverage: 74.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AEGSKINASKNQQDDGYKMFIGGLSWDT-SKKDLTEYLSRFG-EVVDCTIKTDPVT-GRSRGFGFVLFK-
          A.GS.IN.SKNQ..D..KMF.GGLSW.T.SKKDLTEYLS.FG.EVVD.T.KTDPV..GRSRGF.FVLFK.
Retrocopy ARGSTINSSKNQYND-FKMFTGGLSWNT<SKKDLTEYLS*FG<EVVD*TLKTDPVM<GRSRGFRFVLFK>

Parental  DAASVDKVLELKEHKLDGKLIDPKRAKALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMD
          D.A.VDKVLELKEHKLDGKLIDP..AKALK.KEP.KKVFVGGLSPDTSEEQIKEYFGA.GEI.NIELP.D
Retrocopy DDAGVDKVLELKEHKLDGKLIDPQKAKALKEKEPSKKVFVGGLSPDTSEEQIKEYFGACGEIKNIELPVD

Parental  TKTNERRGFCFITYTDEEP-VKKLLESRYHQIGSGKCEIKVAQPKEVYRQQQQQQKG-GRGAAAGGRGGT
          TKTNE...FCFITYT.EEP..K.LLESRY...GS.KCEIKV.QPK.........Q.G.GRG....GRG..
Retrocopy TKTNEGKRFCFITYTHEEP<IKNLLESRYRHTGSRKCEIKVLQPK---KEEEVLQLG<GRGGTR-GRG*G

Parental  RGRGRGQGQN
          .G.....G.N
Retrocopy QGQNWNPGFN

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	105.77 RPM
SRP017611_kidney	0.10 RPM	87.00 RPM
SRP017611_liver	0.00 RPM	55.10 RPM
SRP040447_lung	0.00 RPM	89.38 RPM
SRP040447_skeletal_muscle	0.00 RPM	57.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_264 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_264 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 16 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318, retro_cpor_264 , retro_cpor_274, retro_cpor_567,
Cavia porcellus	ENSCPOG00000020972	1 retrocopy	retro_cpor_1078,
Equus caballus	ENSECAG00000022692	1 retrocopy	retro_ecab_1082,
Microcebus murinus	ENSMICG00000001445	4 retrocopies	retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Sorex araneus	ENSSARG00000009961	1 retrocopy	retro_sara_421,