RetrogeneDB ID: retro_cpor_1426

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_80:3778964..3779756(+)
• Located in intron of: ENSCPOG00000007329

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_1426
AAGAAAGAAATGGAAGAAAGAATAATAACTGTAGACATCCCTGAAGTTCTAAGGAGACAACCTGAAGATGATGGTTACAA
CACTAACAGGAGGAAGCGGTTAGTGAACTCCCATGCAGGCCCACATGCTAACTCCTTTGCAGTCCTGTGGGAAGCATTTT
GCCATCAGTGCAGCCTTGTCAGCCAAGGAGAGGCCTTGGCTCCAGCACACAGAGGCGGGTGCCAATGTGAACACACATTA
TATTATGGCAGGAAACAATGTTGCCCTGAGTAAGGAGGTGGTGGGTGGGCTGAGGGTAACCTTGGATCACACTCTCCCAT
TGCTCCTTCTCGTCCCATATGAACAGGCACCATATAAACAGGTGACTTCAATTAAGCCTTTTGTTTCAATTAAGCAAAGT
GCCACAAACACTGATAGCAGCCAGGAAGGGCTCTCTCTCAACCAGCATTTGTTGACTCCATCCACACTGCAGTCCACAGA
CTGTGATGAGCCTGCACCTTCAAGAGGCGAAACACCAAGCCAGAAGCACTGCAATCCCTGAGGTGGTCCCCGTGTCATAG
CACCCACTGGCACAGGCTGTCCTAGAGCAGCGCCTGGCCCCAGCCCATGTGCGCACAGCAGGACACACCAGCCAACAAGC
CCAGGCTGTGCCTGCATCTGGAAAAGAAGACGCCTGTGAACAGCAGATCACCTTCCTGCACCCCTAATGAGGAAGGGAGG
GCTGTGTTTGCTGGCTTTGAATGGAGAAATGAAATACAGGAGGTGTTCTCCTAGAAGCTTGTACCTGACAAT

Alignment

ORF - retro_cpor_1426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.73 %
• Parental protein coverage: 52.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKEMEERSITIDIPEVLKKQLEDDCYYINRRKRLV-KLPC-QTNIITILESYVKHFAINAAFSATERPRH
          .KEMEER.IT.DIPEVL..Q.EDD.Y..NRRKRLV..LPC.Q....T.L.S..KHFAI.AA.SA.ERP..
Retrocopy KKEMEERIITVDIPEVLRRQPEDDGYNTNRRKRLV<ELPC<QAHMLTPLQSCGKHFAISAALSAKERPWL

Parental  HHAMVHANMNVHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATST
          .H....AN.N.HYI.A..NV.L.KE.V.GLR.T.D.TLPL.LL.PYEQA.YK.VTS.K.F..IK.SAT.T
Retrocopy QHTEAGANVNTHYIMAGNNVALSKEVVGGLRVTLDHTLPLLLLVPYEQAPYKQVTSIKPFVSIKQSATNT

Parental  NRSQEELSPSPPLLNPSTPQSTESQPTTGEPA-TPKRRKAEPEALQSLRRSTRHSTNCDRLSESSASPQP
          ..SQE.LS....LL.PST.QST.......EPA.T.KRR...PEALQSLR.S..HST...RLS.SSA.PQP
Retrocopy DSSQEGLSLNQHLLTPSTLQSTDCD----EPA<TFKRRNTKPEALQSLRWSPCHSTHWHRLS*SSAWPQP

Parental  KRRQQDTSTSMPKLFLHLEKKTPVHSRSSSPIPLTPSKEGSGVFAGFEGRRTNEINEVLSWKLVPDN
          ...QQDT....P.L.LHLEKKTPV.SRS.S....TP..EG..VFAGFE.R..NEI.EV.S.KLVPDN
Retrocopy MCAQQDTPANKPRLCLHLEKKTPVNSRSPS---CTPNEEGRAVFAGFEWR--NEIQEVFS*KLVPDN

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_1426 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1426 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,