RetrogeneDB ID: retro_cpor_296

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:11015670..11016186(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1B2
• Ensembl ID: ENSCPOG00000014496
• Aliases: None
• Description: None

Sequence

>retro_cpor_296
CAAGTTCTCAACAATTACCTGTGGACAAGAGCTTCATTGAGGGAGATACACCCTCACAAGCAGATCCGTGATAGTATTTG
AAGCAGTCTTCAGCCTACAACCTGTTGGCTTGTGTTATATCCTACATTGATATAATCACATGAAGTCTCATGAAAAGGAA
AAGGCCAGCCTGCCAAGAGTGAAGAAAGCTTTAGGCAAGTATGGTTCTGCCAATGTGGAAGACAGCACAGGAAGTAAAGC
TACTAAGAGTAAAGATGATGGTATATCGATCTCTTTGGATCAGGGAGGAGGAGGAAACACAGAAGGTAAGAGAGGAATGA
CTTGCACAGTGTGAATCCAAGAAAGTCATAAGTCCTACACTTGGCAAGTCTTCTGTCTTGCTAGATGTGAAATCTTGGGA
TGATGAGACACATATGGCAAGATTAGGGGAGTGTATCTGAAGCATTCAAGCACATGGCTTAGTCCAGGCTCTTCTGACTG
GTTCCAGTCAGATATAAAATTTAAAAGCTTCAAATA

Alignment

ORF - retro_cpor_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.34 %
• Parental protein coverage: 78.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QVLNDYLADRSYIEGFVP-SQADVAVFEAIACPPPADLFHALRWYNHIKSYEKEKASLPGVKKALGKYGP
          QVLN.YL..R.......P.....V.VFEA.....P..L...L..YNH.KS.EKEKASLP.VKKALGKYG.
Retrocopy QVLNNYLWTRASLREIHP>TSRSVIVFEAVFSLQPVGLCYILH*YNHMKSHEKEKASLPRVKKALGKYGS

Parental  ADVEDTTGSGAADSKDDD-DIDLFGSD-DEEESEEAKRLREERLAQYESKKAKKPALVAKSSILLDVKPW
          A.VED.TGS.A..SKDD...IDLFGS...EEE.......REE.LAQ.ESKK...P.L..KSS.LLDVK.W
Retrocopy ANVEDSTGSKATKSKDDG<YIDLFGSG<EEEETQ---KVREE*LAQCESKKVISPTL-GKSSVLLDVKSW

Parental  DDETDMGKLEECVRSIQADGLVW-GSSK-LVPVGYGIKKLQI
          DDET.M..L.EC..SIQA.GLV..GSS..LVPV.Y.I.KLQI
Retrocopy DDETHMARLGECI*SIQAHGLVQ<GSSD<LVPVRYKI*KLQI

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	56.48 RPM
SRP017611_kidney	0.00 RPM	110.34 RPM
SRP017611_liver	0.00 RPM	127.01 RPM
SRP040447_lung	0.03 RPM	135.69 RPM
SRP040447_skeletal_muscle	0.00 RPM	108.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_296 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_296 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 14 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029635	1 retrocopy	retro_cfam_56,
Callithrix jacchus	ENSCJAG00000005805	2 retrocopies	retro_cjac_176, retro_cjac_341,
Cavia porcellus	ENSCPOG00000014496	4 retrocopies	retro_cpor_1116, retro_cpor_1381, retro_cpor_1407, retro_cpor_296 ,
Gorilla gorilla	ENSGGOG00000007002	2 retrocopies	retro_ggor_134, retro_ggor_2000,
Macropus eugenii	ENSMEUG00000002654	8 retrocopies	retro_meug_1418, retro_meug_1846, retro_meug_1917, retro_meug_240, retro_meug_241, retro_meug_52, retro_meug_775, retro_meug_949,
Myotis lucifugus	ENSMLUG00000016602	8 retrocopies	retro_mluc_1035, retro_mluc_1068, retro_mluc_1104, retro_mluc_1167, retro_mluc_1542, retro_mluc_1578, retro_mluc_1681, retro_mluc_1857,
Oryctolagus cuniculus	ENSOCUG00000009848	4 retrocopies	retro_ocun_1014, retro_ocun_1240, retro_ocun_544, retro_ocun_922,
Oreochromis niloticus	ENSONIG00000017630	1 retrocopy	retro_onil_28,
Ochotona princeps	ENSOPRG00000017163	3 retrocopies	retro_opri_1192, retro_opri_294, retro_opri_748,
Oryzias latipes	ENSORLG00000018533	1 retrocopy	retro_olat_16,
Pongo abelii	ENSPPYG00000013107	7 retrocopies	retro_pabe_1251, retro_pabe_1656, retro_pabe_2163, retro_pabe_2389, retro_pabe_2419, retro_pabe_2746, retro_pabe_2876,
Sarcophilus harrisii	ENSSHAG00000017853	1 retrocopy	retro_shar_208,
Ictidomys tridecemlineatus	ENSSTOG00000005437	3 retrocopies	retro_itri_1263, retro_itri_813, retro_itri_873,
Xiphophorus maculatus	ENSXMAG00000006050	1 retrocopy	retro_xmac_21,