RetrogeneDB ID: retro_cpor_1113

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_47:13991730..13992456(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSCPOG00000014961
• Aliases: None
• Description: None

Sequence

>retro_cpor_1113
GTTGCTCTTTCCCAAAGATCTGTGGCCAAGTCGGCAGATGAAGCTTCTGCAATTGCTGAAAAATTAGGTCCAAACAGATT
GTGACAAAGGCACAGGTTTTGCTAGTAGTAGAAGAAAAGGACCATCTAAAAGTAGACTTAGAGGAAAAATACCGATAGTT
TTCTCTCCAGAAGAAGTGAAAGCTTTTCTTCACAGATGTGGAGAAAGTTGTTTATCAAACAAACTGAAGAAGAAGGTGGA
ACATGTGGTCAACTTTTGATTTGTGAGCGAAACTATCCCAGGAGACAGCACTGCTTTGCAGTAACAATGGAAAGATCATT
GAGGAGTCCTGTATTACTGGGATGTTCACGAGCTGATGTTCACATTGAAGATGTTGCCGCTGAGGGTCCTGATGCCGGAA
GGAAGGAAGCTGCCAATGTTGTATAAAGTATCAGAAAGGAACAAAATGTCCACCTTGCCCAGAAGATGGATTTTCAATGA
ACAGTGTGATTCTGCAGCACAAAACATTGTCAAGTTTTACAACTGTTTTCTAAAATATAACGCAACCGTGGTAGAAATGA
ATCCAGTGGTAGGAGGCTCAGGGAGAGCTGTGCTCTGCATGGATGCAAAGATTAATTTTGATTCTAATTTAGCCTGTTGC
CAAAAGGAAATTACTGATCTCCAGGACGGATGCAGGAAGACAAAAGAGGCTAAGATACAACTAAGGCAAGTCTTGTCTGC
ATTGGC

Alignment

ORF - retro_cpor_1113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.96 %
• Parental protein coverage: 56.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VSIPKGYVAKSADEAYAIAKKLG-SKDVVIKAQVL-AGGRGKGTFESGLKGGVKIVFSPEEAKAV-SSQM
          V......VAKSADEA.AIA.KLG.SK..V.KAQVL.A..R.KG...S.L.G...IVFSPEE.KA..SSQM
Retrocopy VALSQRSVAKSADEASAIAEKLG<SKQIVTKAQVL<ASSRRKGPSKSRLRGKIPIVFSPEEVKAF<SSQM

Parental  IGKKLFTKQTGAKGRICNQVLICERKYPRREYYFAITMERSFQGPVLIGSSQGGVNIEDVAAETPDAIVK
          ...KLF.KQT...G..C.Q.LICER.YPRR...FA.TMERS...PVL.G.S...V.IEDVAAE.PDA..K
Retrocopy -WRKLFIKQTEEEGGTCGQLLICERNYPRRQHCFAVTMERSLRSPVLLGCSRADVHIEDVAAEGPDAGRK

Parental  EPVDIVEGIKKEQAVQLATKM-GFPANIV-DSAAENMVKLYNLFLKYDATMVEINPMVEDSDGAVLCMDA
          E....V..I.KEQ.V.LA.KM.GF..N.V.DSAA.N.VK.YN.FLKY.AT.VE.NP.V..S..AVLCMDA
Retrocopy EAANVV*SIRKEQNVHLAQKM<GFSMNSV<DSAAQNIVKFYNCFLKYNATVVEMNPVVGGSGRAVLCMDA

Parental  KINFDSNSAYRQKKIFDLQDW-TQEDERDRDAAKANLNYIG
          KINFDSN.A..QK.I.DLQD...QED.R..D..KA.L..IG
Retrocopy KINFDSNLACCQKEITDLQDG<MQEDKRG*DTTKASLVCIG

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	0.06 RPM	66.49 RPM
SRP017611_kidney	0.00 RPM	72.34 RPM
SRP017611_liver	0.00 RPM	24.20 RPM
SRP040447_lung	0.00 RPM	24.21 RPM
SRP040447_skeletal_muscle	0.00 RPM	105.23 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1113 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1113 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 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113 ,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,