RetrogeneDB ID: retro_cpor_622

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_20:19910769..19911326(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKTIP
• Ensembl ID: ENSCPOG00000006523
• Aliases: None
• Description: None

Sequence

>retro_cpor_622
CCATCGTATCACTCTGCGTTAATGTGGTTTGGAGCAATACTCATACGGCACGGGCTTTGTCAAGATGGCATGTTCAAGTT
TATAGTTCACATCCCACATGGTGACTGTCCATGGTTGGTGTTTGCTATTCCCGTCTTTTACCCACTAGTTGATCCCGCCT
CAGATGAACTGTGTGTGAAGGGAGCATTTGCGCAATGGAGGTGGAACCATAATCTTATTTGGCAGGTATTGATGTATGCA
GGGAGAGTTTTCTATAAGATTGAGACAGGAAGCCCCTTGAATCCAGAAGTTGCAGCCTTGCATGAAAAAGATGTTCACCT
TTTTAAAAACAAAGTGATTGACCCTGAAGTGTGCACTTCTCATTTGTTTGAACAACCTAAAATAGAAGACCTCCTATGCA
ATTAGCTTTTCTCCATGGAATCCTTCTGTGCACAGTGAAGCCAGAGAGAAGATGCTGACTCAGAAACCTGAAGAACAACA
CAGTAAAAAGTGTTCATGTTGCTGGCCTGTCATGAGTAAAGCCTGGCTCAGTATAACCTTTCACTAAAGAAGAAAAA

Alignment

ORF - retro_cpor_622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.04 %
• Parental protein coverage: 65.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSYRSALMWFGVIFIRHGLYQDGVFKFTVYIPDNYPDGDCPRLVFDIPVFHPLVDPTSGELDVKRAFAKW
          PSY.SALMWFG.I.IRHGL.QDG.FKF.V.I....P.GDCP.LVF.IPVF.PLVDP.S.EL.VK.AFA.W
Retrocopy PSYHSALMWFGAILIRHGLCQDGMFKFIVHI----PHGDCPWLVFAIPVFYPLVDPASDELCVKGAFAQW

Parental  RRNHNHIWQVLMYARRVFYKIDTASPLNPEAAVLYEKDVHLFKSKVVDSVKVCTSRLFEQPKIED-PYAI
          R.NHN.IWQVLMYA.RVFYKI.T.SPLNPE.A.L.EKDVHLFK.KV.D...VCTS.LFEQPKIED..YAI
Retrocopy RWNHNLIWQVLMYAGRVFYKIETGSPLNPEVAALHEKDVHLFKNKVIDP-EVCTSHLFEQPKIED>SYAI

Parental  SFSPWNPSVHDEAREKMLTQKKPEEQH-KSVHVAGLSWVKPGSVQPFSKEEK
          SFSPWNPSVH.EAREKMLTQK..E....KSVHVAGLS.VKPGSV.PF.KEEK
Retrocopy SFSPWNPSVHSEAREKMLTQKPEEQHS>KSVHVAGLS*VKPGSV*PFTKEEK

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	0.92 RPM	37.90 RPM
SRP017611_kidney	0.94 RPM	25.44 RPM
SRP017611_liver	0.13 RPM	11.75 RPM
SRP040447_lung	1.31 RPM	16.22 RPM
SRP040447_skeletal_muscle	0.26 RPM	15.98 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_622 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_622 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.

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016345	1 retrocopy	retro_amel_392,
Canis familiaris	ENSCAFG00000009500	1 retrocopy	retro_cfam_1826,
Choloepus hoffmanni	ENSCHOG00000013690	2 retrocopies	retro_chof_2533, retro_chof_629,
Callithrix jacchus	ENSCJAG00000001498	1 retrocopy	retro_cjac_2895,
Cavia porcellus	ENSCPOG00000006523	1 retrocopy	retro_cpor_622 ,
Dasypus novemcinctus	ENSDNOG00000004906	4 retrocopies	retro_dnov_1376, retro_dnov_1776, retro_dnov_2080, retro_dnov_756,
Equus caballus	ENSECAG00000020381	1 retrocopy	retro_ecab_504,
Homo sapiens	ENSG00000166971	2 retrocopies	retro_hsap_1458, retro_hsap_3152,
Gorilla gorilla	ENSGGOG00000014821	1 retrocopy	retro_ggor_1122,
Microcebus murinus	ENSMICG00000010810	3 retrocopies	retro_mmur_124, retro_mmur_333, retro_mmur_985,
Microcebus murinus	ENSMICG00000016793	1 retrocopy	retro_mmur_1191,
Monodelphis domestica	ENSMODG00000025788	1 retrocopy	retro_mdom_1881,
Nomascus leucogenys	ENSNLEG00000001106	1 retrocopy	retro_nleu_2660,
Otolemur garnettii	ENSOGAG00000014495	1 retrocopy	retro_ogar_365,
Oryzias latipes	ENSORLG00000013747	1 retrocopy	retro_olat_30,
Pongo abelii	ENSPPYG00000007351	2 retrocopies	retro_pabe_1204, retro_pabe_1205,
Pan troglodytes	ENSPTRG00000008116	1 retrocopy	retro_ptro_2282,
Rattus norvegicus	ENSRNOG00000011956	1 retrocopy	retro_rnor_1611,
Tupaia belangeri	ENSTBEG00000017105	5 retrocopies	retro_tbel_1063, retro_tbel_2864, retro_tbel_3350, retro_tbel_4130, retro_tbel_853,
Tursiops truncatus	ENSTTRG00000012705	1 retrocopy	retro_ttru_348,