RetrogeneDB ID: retro_cpor_1262

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_60:7747011..7747955(+)
• Located in intron of: ENSCPOG00000013410

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_1262
AATAGTTTCAACTTCTTCCTTACTGTTGAAAGAATTAGACAACTTTTGCCCTCACACATGGGAAGACATTTCTATCAAAG
GAAAAAAGTTCCAGGCCCTGTAAATCTTCTGGGCAAGAATTTATCAGAAAAGATCAACAACTCCATAGAGGGACTGTCTT
AAACATCTCCAAAAGTGGTTCTTGCAGTTCTGTATGCATTGGCCACACTGGAATGTGGGCTCAGGACATCACTGAAAACA
TTGTTGCTGTGGCAGAAAGTCTTTCAAAAAAATTGCCAGAGAAGTGGAAAAGCGAAACTCTTGTGTGTGAAAACTGGGAA
GTCAGTTCCTTTCCCATCTTTCCTTATTTATCTCTTATCGGAATGAAACCAACAAAATGTTCATCCGTGAACTGAAGGAA
AAAGAGGTTAAGACTAAAGTGAGAGCGAAAAGTTTGTGAAAAACAGAAGTTGAACAGGGAAAAGGAAAAGTTAAAGGGAA
AAGCTAAGAAGGCTACATCAGTGCTAGCTAAAGTTGGCGAGGCGCCTAAAGCTTAAGGTGCTTCCGTGAAGAGCAGCAGG
CTGCAGAAGAAAAAGATTGGCAAGTGAAAACCCAAGTTAAAGTGACAAATGAATCTGACGATGAAATTCCACAACTGGTA
CCTAAAGGTAAAAATCCAGTAAAAGAAAATGTTGAGGTACAAAAACATATCACAGGGAAGAAGTCTCCAAATAAGAGTCC
TGGTCCCAAAACACCACAGGACAAGAAGAGAAAAGCCCTGATGGCTCCTGAGATCCCAGACACAAGTCTAAGGAAGAAGC
CAAAAATGGGACAGGAGAAGAAGCAGCAAAGAAAATCCTCACCAGGGAAGACAGACTCCCAAAGAGCAGGAGGCCAAGCT
CTTCACTACTGTAATAAATATTGTAAGGGAAGATACCCACACCCCTAAACAATTGCCAAAAGAA

Alignment

ORF - retro_cpor_1262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.32 %
• Parental protein coverage: 71.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NSFDFFLTDERIRRLLPSHIGRHFYQRKKVPVSVNLLAKNLSEEINNSLG-GTVLNISKSGSCSSVRIGH
          NSF.FFLT.ERIR.LLPSH.GRHFYQRKKVP..VNLL.KNLSE.INNS...GTVLNISKSGSCSSV.IGH
Retrocopy NSFNFFLTVERIRQLLPSHMGRHFYQRKKVPGPVNLLGKNLSEKINNSIE<GTVLNISKSGSCSSVCIGH

Parental  TGMRAQDITENIVAVAEGLSKKLPEKWESVKLLFVKTGKSVSLPIF-SSFVSCQNETNKMLIRKLKEKEA
          TGM.AQDITENIVAVAE.LSKKLPEKW.S...L........S.PIF.S.F.S..NETNKM.IR.LKEKE.
Retrocopy TGMWAQDITENIVAVAESLSKKLPEKWKS-ETLVCENWEVSSFPIF<SLFISYRNETNKMFIRELKEKEV

Parental  KRKEKEQKLREKRKLKKEKRK-LKGKAKKVTSVLTKGGVAPQTKGASAKSRRSQKKKTGK-VKTQVKVTN
          K.K.....L..K......K.K.LKGKAKK.TSVL.K.G.AP...GAS.KS.R.QKKK.GK.VKTQVKVTN
Retrocopy KTKVRAKSL-*KTEVEQGKGK>LKGKAKKATSVLAKVGEAPKA*GASVKSSRLQKKKIGK<VKTQVKVTN

Parental  ESDDEIPQLVPIGETPVKENVEVQKHITGKKSPKKSPGPKTPQGKKRKALPVPEIPDAGPGKKPKMGQEK
          ESDDEIPQLVP.G..PVKENVEVQKHITGKKSP.KSPGPKTPQ.KKRKAL..PEIPD....KKPKMGQEK
Retrocopy ESDDEIPQLVPKGKNPVKENVEVQKHITGKKSPNKSPGPKTPQDKKRKALMAPEIPDTSLRKKPKMGQEK

Parental  --QRKSSPGKKDL-RQTPKKPEAKLFTTANKSTRKAPQTPKQ
          ..QRKSSPGK.D.......K............T....Q.PK.
Retrocopy KQQRKSSPGKTDS>KEQEAKLFTTVINIVREDTHTPKQLPKE

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_1262 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1262 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 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,