RetrogeneDB ID: retro_cpor_1379

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_78:3757643..3758395(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELAVL4
• Ensembl ID: ENSCPOG00000002044
• Aliases: None
• Description: None

Sequence

>retro_cpor_1379
ATAATTAGTGTCATGGAGCCTCAGGTGTCAAATAGCCCAACATCCAATACAAACAATGGACCCTCCAACAACAACATAAA
ATGTCCTTCTCCCAGGCAGACAGGGACAGCCACAGATGACAGCAAAATTAACTTCATCATCAACTATTTACTCCAAAATA
TGACCCAAGCGGAATTCAGGATTCTCTCCAGTAGCACTGGTGAAATAGAATCCTGCAAACTTGTGAGAGACAAAATTAAA
GGACAGAGTTTAGGGTATGGATTTGTTAAATATATTGATCCAAAGGATGCAGAGAAAGCCATCAACACTTTAAATTGATT
CCGAGTTCAAACCAAAACCGTAATGATCTTATATGCCTGGCCAAGCTTAGCTTCAATCAGGGAATGCTAACCTCCATGTT
AGTGAGCTCCCCAAAACCATGACCCAAAAGGAACTGAAGCAGCTTTTCTCACAATATGGTCAGATTATTACCTCATGAAT
CCTGGTTGGTCAAGTTACAGGAGTGTCTAAAGGGATGGGATTCCACTTTGATAAGAGAATCAAGGCAGAATAAGCCATTA
AAGGGCCGAATGGCCAGAAGCCCAGTGGCACTACAGAACTGATTATTGTGAATTTTGCCAACAACCCCAGCCAAAATTCG
AGCCAGACCCTGCTTTTCCAGATGTACTAGTCCCCCAGCTGATGCTAACTTGGCCCACTCCTTCACCAGCGCTCGGACGT
TGAGGCTGAACAATTTGCTTAATGTGGCCTAT

Alignment

ORF - retro_cpor_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.7 %
• Parental protein coverage: 69.15 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IISTMEPQVSNGPTSNTSNGPSSNNRNCPSPMQTGAATDDSKTNLIVNYLPQNMTQEEFRSLFGSIGEIE
          IIS.MEPQVSN.PTSNT.NGPS.NN..CPSP.QTG.ATDDSK.N.I.NYL.QNMTQ.EFR.L..S.GEIE
Retrocopy IISVMEPQVSNSPTSNTNNGPSNNNIKCPSPRQTGTATDDSKINFIINYLLQNMTQAEFRILSSSTGEIE

Parental  SCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRD-ANLYVSGLPKT
          SCKLVRDKI.GQSLGYGFV.YIDPKDAEKAINTLN..R.QTKT....YA.PS.ASIR..ANL.VS.LPKT
Retrocopy SCKLVRDKIKGQSLGYGFVKYIDPKDAEKAINTLN*FRVQTKTVMILYAWPSLASIRE>ANLHVSELPKT

Parental  MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFANN
          MTQKEL.QLFSQYG.IITS.ILV.QVTGVS.G.GF..FDKRI.AE.AIKG.NGQKPSG.TE.I.V.FANN
Retrocopy MTQKELKQLFSQYGQIITS*ILVGQVTGVSKGMGF-HFDKRIKAE*AIKGPNGQKPSGTTELIIVNFANN

Parental  PSQKSSQALLSQLYQSPNRRYPGPLHHQ-AQRFRLDNLLNMAY
          PSQ.SSQ.LL.Q.Y.SP.....GPL.HQ.A...RL.NLLN.AY
Retrocopy PSQNSSQTLLFQMY*SPS*C*LGPLLHQ>ARTLRLNNLLNVAY

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	49.64 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.17 RPM
SRP040447_lung	0.00 RPM	0.05 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1379 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1379 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002464	1 retrocopy	retro_chof_1943,
Cavia porcellus	ENSCPOG00000002044	1 retrocopy	retro_cpor_1379 ,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Macropus eugenii	ENSMEUG00000007145	1 retrocopy	retro_meug_426,
Sarcophilus harrisii	ENSSHAG00000013832	1 retrocopy	retro_shar_78,