RetrogeneDB ID: retro_cpor_1423

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_80:3543209..3544049(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSCPOG00000004692
• Aliases: None
• Description: None

Sequence

>retro_cpor_1423
CGAACTCCCATGCAGGCCCACATGCTAACTCTTTTGCAGTCCTGTGGGAAGCACTTTGCCATCCGTGCAGCCTCATCAGC
CAAGCAGAGGCTCCAGCACACCGCGGCAGGTGCTAATGTGAACATGCATTTTATTCCAGCAGAAAACAATGTTGCCCTGA
GTAAGGAGGTGGTGGGTGGGCTGAGGGTAACCTTTGATCACACTCTCGCATGGCTCTTGCTCAACCTGTATGAACAGGCA
CCATATAGAAAGGTGACTTCAATTATGCCTTTTGTTTCAATTAAACAAAGTGCCATAAACACTGCTAAGAGCTAGGAAGG
GATTTCTCTCAATCCACCTTTGTTGAGTCTGTCCACACTGCAGTCCATAGATTGTGACGAGCCTGCATCCCTAAGAGGTA
AAAAACCAAGCCAGAAGCACTGCAGTCCCTGAGGTGGTTCCCGTGTCATAGCACCCACTGCCACAGGCTGTCCTAGAGCA
GCACCTGGCCCCAGCCCATGTGCCCACACAGGACACATCAGCCAACAAGCCCAGGCTGTGCAAGCATCTGGAAAAGAACA
TGCCTGTGAACAGCAGATCATCTTCCTGCATGCCTGTGACACCTAATGAGGAAGGACAGGCTATGTTTGCTGATTTTAAA
GGGAGAAGTGAAATAGAGGAGGTTTTCTTCTAGCATCTTCTGCCTGACAATTTTACCCTCCAAGTGACAAGCCACCTCCA
CCCTCTTACATTTATGGTGCACAAGATTTGGTATGATTGTTTATAAAACTTCCAGAAATCCTGGGAAAAGCATCCTTTCC
TGAGAATGATCCCAAGGGTTTCCTGAAGCACTTGAATCTC

Alignment

ORF - retro_cpor_1423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.11 %
• Parental protein coverage: 55.38 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLPCQTNIITILESYVKHFAINAAFSATERPRHHHAMVHANMNVHYIPAEKNVDLCKEMVDGLRITFDYT
          ..P.Q....T.L.S..KHFAI.AA.SA..R..H..A...AN.N.H.IPAE.NV.L.KE.V.GLR.TFD.T
Retrocopy RTPMQAHMLTLLQSCGKHFAIRAASSAKQRLQHTAA--GANVNMHFIPAENNVALSKEVVGGLRVTFDHT

Parental  LPLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSPSPPLLNPSTPQSTESQPTTGEPAT-PKR
          L...LL..YEQA.Y.KVTS...F..IK.SA..T..S.E..S..PPLL..ST.QS........EPA..PKR
Retrocopy LAWLLLNLYEQAPYRKVTSIMPFVSIKQSAINTAKS*EGISLNPPLLSLSTLQSIDCD----EPAS<PKR

Parental  RKAEPEALQSLRRSTRHSTNCDRLSESSASPQPKRRQQ-DTSTSMPKLFLHLEKKTPVHSRSSSPIPLTP
          .K..PEALQSLR....HST.C.RLS.SS..PQP......DTS...P.L..HLEK..PV.SRSSS..P.TP
Retrocopy *KTKPEALQSLRWFPCHSTHCHRLS*SSTWPQPMCPHR<DTSANKPRLCKHLEKNMPVNSRSSSCMPVTP

Parental  SKEGSGVFAGFEGRRTNEINEVLSWKLVPDNYP-PGDQPP-PPSYIYGAQHLLRLFVKLPEILGKMSFSE
          ..EG...FA.F.GR...EI.EV....L.PDN...P....P.PPSYIYGAQ.L..LF.KLPEILGK.SF.E
Retrocopy NEEGQAMFADFKGR--SEIEEVFF*HLLPDNFT<PPSDKPPPPSYIYGAQDLV*LFIKLPEILGKASFPE

Parental  KNLKALLKHFDL
          ...K..LKH..L
Retrocopy NDPKGFLKHLNL

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	12.77 RPM
SRP017611_kidney	0.00 RPM	17.38 RPM
SRP017611_liver	0.00 RPM	10.75 RPM
SRP040447_lung	0.00 RPM	19.22 RPM
SRP040447_skeletal_muscle	0.00 RPM	22.59 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1423 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1423 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 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009278	1 retrocopy	retro_btau_883,
Callithrix jacchus	ENSCJAG00000001061	1 retrocopy	retro_cjac_1490,
Cavia porcellus	ENSCPOG00000004692	5 retrocopies	retro_cpor_1423 , retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens	ENSG00000005302	2 retrocopies	retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla	ENSGGOG00000006582	2 retrocopies	retro_ggor_1820, retro_ggor_2749,
Macaca mulatta	ENSMMUG00000002689	2 retrocopies	retro_mmul_2362, retro_mmul_972,
Monodelphis domestica	ENSMODG00000017350	1 retrocopy	retro_mdom_1422,
Pongo abelii	ENSPPYG00000020123	2 retrocopies	retro_pabe_2166, retro_pabe_3353,
Pan troglodytes	ENSPTRG00000021662	2 retrocopies	retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus	ENSPVAG00000005000	1 retrocopy	retro_pvam_203,
Sorex araneus	ENSSARG00000008477	1 retrocopy	retro_sara_139,
Tarsius syrichta	ENSTSYG00000012788	4 retrocopies	retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,