RetrogeneDB ID: retro_cpor_822

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:15410349..15411125(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSL1D1
• Ensembl ID: ENSCPOG00000010630
• Aliases: None
• Description: None

Sequence

>retro_cpor_822
TCAACTCCCACAGAGCTGACCTCACTGGAGCAGCCTGACAAAAAACAGGTTAGAAAGGCAGTGGAAGCTTTGTTGACACA
GTGAAAGTGCAGGAAGAACAAAAATGGATTGCTTTTGAATGAGAATGAAAATTTATTTTTAATGGTGGTATTATGGAAAA
TTCCAGGAAAAGAGCTGAGGGTCAGGTTGTCCTTGCCTCCCAGTATTCAATCAGACTTGTCAGAAATCTGTTTATTTACC
AAGGATGAACTCCAGTCAACTGAAACTGAGACAGAACACTTTTATAGAAAGCTTTTGAACAAGCATGGAATCAAAACAGT
TTCTCAGATTAGCCCTTTTCAAACTTTAAAAACAGAATATAAAGCTTATGAAGCCAAACTCCTACTCCTAAATAGTTTTG
ACTTCTTCCTTAGTGATGAAAGAATTATGTGGCTTTTGCCCTTGCAAATAGAAAAGCATTTCTATCGAAGGAAAAAAAGT
TCCAGTATCTGTAAATCTTCTGGCCAAGAATTTATCAGAAGAGATCAACAACTCCCTTGGTGGGACTGTCTTAAACATCT
ACAAACGTGATTCTTACAGCACTATATGCATTGGTCACGTCGGAATGTGAGCTCAAGACGTCACCGACATTTTGTTGCTG
TGGCAGAAAATCTTTCAGAGCAATTGCCAGAGAAGTGGAAAGTGTGAAACTTCTATCTGTGAAAACTGGAAGTTGGTTTC
CCTTCCCACTTTTTCTATCTATCTTTTATCAGAATGAAACCAAGAAAATGTTCATC

Alignment

ORF - retro_cpor_822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.29 %
• Parental protein coverage: 92.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ATSSELTSLEQLDKKQIRKAVEALLTQSKSRKNKNGLLLNENESLFLMVVLWKIPGKELKVKLLLPHHIR
          .T..ELTSLEQ.DKKQ.RKAVEALLTQ.K.RKNKNGLLLNENE.LFLMVVLWKIPGKEL.V.L.LP..I.
Retrocopy STPTELTSLEQPDKKQVRKAVEALLTQ*KCRKNKNGLLLNENENLFLMVVLWKIPGKELRVRLSLPPSIQ

Parental  SDLSEICLFTKDELQSAE-QTERFYRKLLNKHGIKTISRIIPFRTLKTEYKAYESKLQLLNSFDFFLTDE
          SDLSEICLFTKDELQS.E..TE.FYRKLLNKHGIKT.S.I.PF.TLKTEYKAYE.KL.LLNSFDFFL.DE
Retrocopy SDLSEICLFTKDELQSTETETEHFYRKLLNKHGIKTVSQISPFQTLKTEYKAYEAKLLLLNSFDFFLSDE

Parental  RIRRLLPSHIGRHFYQR-KKVPVSVNLLAKNLSEEINNSLGGTVLNISKSGSCSSVRIGHTGMRAQDITE
          RI..LLP..I..HFY.R.KKVPVSVNLLAKNLSEEINNSLGGTVLNI.K..S.S...IGH.GM.AQD.T.
Retrocopy RIMWLLPLQIEKHFYRR>KKVPVSVNLLAKNLSEEINNSLGGTVLNIYKRDSYSTICIGHVGM*AQDVTD

Parental  -NIVAVAEGLSKKLPEKW-ESVKLLFVKTGKSVSLPIFSSFVSCQNETNKMLI
          ...VAVAE.LS..LPEKW.ESVKLL.VKTG.....P.F.S....QNET.KM.I
Retrocopy <HFVAVAENLSEQLPEKW<ESVKLLSVKTGSWFPFPLFLS-IFYQNETKKMFI

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	31.23 RPM
SRP017611_kidney	0.00 RPM	35.70 RPM
SRP017611_liver	0.00 RPM	26.29 RPM
SRP040447_lung	0.00 RPM	21.66 RPM
SRP040447_skeletal_muscle	0.00 RPM	19.25 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_822 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_822 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018865	2 retrocopies	retro_cfam_1937, retro_cfam_691,
Choloepus hoffmanni	ENSCHOG00000010827	2 retrocopies	retro_chof_1617, retro_chof_852,
Callithrix jacchus	ENSCJAG00000008375	1 retrocopy	retro_cjac_2154,
Cavia porcellus	ENSCPOG00000010630	3 retrocopies	retro_cpor_1262, retro_cpor_276, retro_cpor_822 ,
Loxodonta africana	ENSLAFG00000013664	1 retrocopy	retro_lafr_364,
Myotis lucifugus	ENSMLUG00000000784	1 retrocopy	retro_mluc_1309,
Monodelphis domestica	ENSMODG00000029494	2 retrocopies	retro_mdom_1240, retro_mdom_573,
Otolemur garnettii	ENSOGAG00000015151	1 retrocopy	retro_ogar_2604,
Rattus norvegicus	ENSRNOG00000048608	1 retrocopy	retro_rnor_2771,
Sarcophilus harrisii	ENSSHAG00000016705	1 retrocopy	retro_shar_836,