RetrogeneDB ID: retro_cpor_901

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_32:19594454..19594842(-)
• Located in intron of: ENSCPOG00000000079

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYB
• Ensembl ID: ENSCPOG00000003213
• Aliases: None
• Description: None

Sequence

>retro_cpor_901
AAAGATTGCAAAAATTACCAAAAATTATGCTCAGGAATATGTGAGTTCACAGGCTTTGTAACAGCTGAGGCCAGTGAGGG
GTGCTACCAGGAGAAGTGAAAGACAATCAAAGGATAATGCATTCTCTTTGCCATGTCCACCCTAAGCTTCAGCAGCTATG
AGGAACCCCTGAAGTCGTACCTTCTTCTGAAGTTTAGAGAGGCTGTGAAAGAGAGAAGGAAATTGGAGGAGTGGCCCAGT
AATGGATGGACTCAGTGAGGAGCACATGGAAGAGGCCCTCACTAACCAGTTACCAACTGGTTTGACTGCAGATGGGTGAC
TACAAAATGTTACTGTTTATACAACATCCTATCAATGGATTTCTAGTGTTCGGAAGATTCAGTTTTCA

Alignment

ORF - retro_cpor_901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 61.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDAKECVQEC--VSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLY-LQKFREAMK
          KD.K.....C....EF..F.T.EASE.C.QEK.KTI.G..ILFAMSTL.F.SY.EPLK.Y.L.KFREA.K
Retrocopy KDCKNYQKLCSGICEFTGFVTAEASEGCYQEK*KTIKG*CILFAMSTLSFSSYEEPLKSYLLLKFREAVK

Parental  -GEKGIGGAV-TAADGLGEELTEEAFTNQLPAGLITADGQQQNVMVYTTSYQQISGVQQIQFS
          ..EK.IGG......DGL.EE..EEA.TNQLP.GL.TADG..QNV.VYTTSYQ.IS.V..IQFS
Retrocopy <REKEIGGVA<PVMDGLSEEHMEEALTNQLPTGL-TADG*LQNVTVYTTSYQWISSVRKIQFS

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	9.09 RPM
SRP017611_kidney	0.00 RPM	8.90 RPM
SRP017611_liver	0.00 RPM	5.18 RPM
SRP040447_lung	0.00 RPM	10.47 RPM
SRP040447_skeletal_muscle	0.01 RPM	17.96 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_901 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_901 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 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006686	1 retrocopy	retro_amel_940,
Bos taurus	ENSBTAG00000030744	1 retrocopy	retro_btau_1681,
Canis familiaris	ENSCAFG00000029177	1 retrocopy	retro_cfam_1677,
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901 ,
Dasypus novemcinctus	ENSDNOG00000009984	3 retrocopies	retro_dnov_1536, retro_dnov_758, retro_dnov_855,
Felis catus	ENSFCAG00000026471	1 retrocopy	retro_fcat_207,
Homo sapiens	ENSG00000120837	2 retrocopies	retro_hsap_2827, retro_hsap_4047,
Gorilla gorilla	ENSGGOG00000008866	1 retrocopy	retro_ggor_2714,
Myotis lucifugus	ENSMLUG00000005468	1 retrocopy	retro_mluc_1764,
Macaca mulatta	ENSMMUG00000022570	3 retrocopies	retro_mmul_1433, retro_mmul_2119, retro_mmul_2335,
Mustela putorius furo	ENSMPUG00000012064	3 retrocopies	retro_mputfur_1531, retro_mputfur_1563, retro_mputfur_1567,
Nomascus leucogenys	ENSNLEG00000006543	2 retrocopies	retro_nleu_1203, retro_nleu_2061,
Oryctolagus cuniculus	ENSOCUG00000004415	4 retrocopies	retro_ocun_1334, retro_ocun_1816, retro_ocun_1824, retro_ocun_1845,
Ochotona princeps	ENSOPRG00000008117	2 retrocopies	retro_opri_36, retro_opri_657,
Pongo abelii	ENSPPYG00000004892	3 retrocopies	retro_pabe_2201, retro_pabe_2803, retro_pabe_3319,
Ictidomys tridecemlineatus	ENSSTOG00000005279	1 retrocopy	retro_itri_1851,
Tupaia belangeri	ENSTBEG00000005731	1 retrocopy	retro_tbel_4360,