RetrogeneDB ID: retro_cpor_1344

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_70:2066036..2067167(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGGT1B
• Ensembl ID: ENSCPOG00000002443
• Aliases: None
• Description: None

Sequence

>retro_cpor_1344
ATGGCGGCCACTGAGCACAACCAGCGGCTGGTGGGGAGCAGTGAGAGAGAGCAACTAGACTTCTTGCTGGACCAACATGT
GTGGTTTTTCCAGCGATGCCTTCAGGTTCTGCCAGAGTATTATTCTTCTCTCAAGAACAGCAGGTTGACAATTGCATTTC
TTGCACTCTCTGGACTAGGCATGTTGGACTCCTTAGATGTAGTGAACAAAGATGATAGAATAGAATGGATTTACTCCCTG
CAGATTCTTTCCACAGAAGACAGATCAAATCTAAATTGCTGTGGCTTCCAAGGCTCTTCGTATCTGGGTATTCCATTCAA
CTCATCAAGGAATCCTGGGACAGCTCATCCATATGTAGTGGTCACATAACAATGACCTACACTGGCCTTTCATGGCTAGT
TATTCTTGGAGATGATTTAAACTGAGTAAATAAAGAAGCTTGTTTAGTGGGTTTGAGAGCCCTTCAATTGGAAGATGAAA
GTTTCTGTGCGGAACCTGAAGGCAGTGAAAATGGCATGCGATTTGTGTACTGTGCTTCCTGTATTTGCTATAGGCTCAAT
GACTGGTCAGGCATGGGTGTTAAAAAAGCCATCCACTATCTTAGAAGAAGTATGTCCTATGACAATGGGCTGGCACAGGG
AACAGGACTTGAATCTCATGGAGAATCCACCTTCTGTGGTATTTCATTACTATACCTAATGGGTAAACTAGAAGAAGTTT
TTTTCAGAAAAAGAACTGAACAGGATAAAGAGGTGGTGTATAACGAGGTAACAAAATGGTTATCACAGAAAACCTGATAA
GCCAGTGGACACCTGCTACTCATTTTGGGTGGGAGCAACTCTGAAGCTTCTGAAAATTTTCCAGTACACTAACTTTGAGA
AAAATAGAAATTACATCTTACCAACTCAAGATCACCTTGTAGGCTTTGCCAAATAGCCAGACAGTCATCCAGATGCTTTG
CATGCATACTTCTGGATCTGTGGCCTTTCACTAATGGAGGAAAGTGGGGTTTGTAAAGTTCATCCCACTCTGAATGTAAG
CACACAAACTCCTGAACGCCTTCGAGATCTCCATCAAAGCTGGGAATCCAAGGACTCTAAACAAAGCTCAGAGAATGTCC
ATGTCTCCAAA

Alignment

ORF - retro_cpor_1344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAATE-DERLVGSGEGERLDFLRDRHVRFFQRCLQVLPERYSSLETSRLTIAFFALSGLDMLDSLDVVNK
          MAATE...RLVGS.E.E.LDFL.D.HV.FFQRCLQVLPE.YSSL..SRLTIAF.ALSGL.MLDSLDVVNK
Retrocopy MAATEHNQRLVGSSEREQLDFLLDQHVWFFQRCLQVLPEYYSSLKNSRLTIAFLALSGLGMLDSLDVVNK

Parental  DDIIEWIYSLQVLPTEDRSNLNRCGFRGSSYLGIPFNPSKSPGTAHPYD-SGHIAMTYTGLSCLVILGDD
          DD.IEWIYSLQ.L.TEDRSNLN.CGF.GSSYLGIPFN.S..PGTAHPY..SGHI.MTYTGLS.LVILGDD
Retrocopy DDRIEWIYSLQILSTEDRSNLNCCGFQGSSYLGIPFNSSRNPGTAHPYV<SGHITMTYTGLSWLVILGDD

Parental  LSRVNKEACLAGLRALQLEDGSFCAVPEGSENDMRFVYCASCICYMLNDWSGMDVKKAISYIRRSMSYDN
          L..VNKEACL.GLRALQLED.SFCA.PEGSEN.MRFVYCASCICY.LNDWSGM.VKKAI.Y.RRSMSYDN
Retrocopy LN*VNKEACLVGLRALQLEDESFCAEPEGSENGMRFVYCASCICYRLNDWSGMGVKKAIHYLRRSMSYDN

Parental  GLAQGAGLESHGGSTFCGIASLCLMGKLEEV-FSEKELNRIKRWCIMRQQNGYHGRPNKPVDTCYSFWVG
          GLAQG.GLESHG.STFCGI..L.LMGKLEEV.FSEKELNRIKRWCI.R.QNGYH..P.KPVDTCYSFWVG
Retrocopy GLAQGTGLESHGESTFCGISLLYLMGKLEEV>FSEKELNRIKRWCITR*QNGYHRKPDKPVDTCYSFWVG

Parental  ATLKLLKIFQYTNFEKNRNYILSTQDRLVGGFAKWPDSHPDALHAYFGICGLSLMEESGICKVHPALNVS
          ATLKLLKIFQYTNFEKNRNYIL.TQD.LV.GFAK.PDSHPDALHAYF.ICGLSLMEESG.CKVHP.LNVS
Retrocopy ATLKLLKIFQYTNFEKNRNYILPTQDHLV-GFAK*PDSHPDALHAYFWICGLSLMEESGVCKVHPTLNVS

Parental  TRTSERLRDLHQSWESKDSKQSSEDVHDSK
          T.T.ERLRDLHQSWESKDSKQSSE.VH.SK
Retrocopy TQTPERLRDLHQSWESKDSKQSSENVHVSK

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	3.05 RPM
SRP017611_kidney	0.10 RPM	5.97 RPM
SRP017611_liver	0.00 RPM	4.44 RPM
SRP040447_lung	0.00 RPM	5.83 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1344 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1344 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016700	1 retrocopy	retro_cjac_1058,
Cavia porcellus	ENSCPOG00000002443	1 retrocopy	retro_cpor_1344 ,
Homo sapiens	ENSG00000164219	2 retrocopies	retro_hsap_675, retro_hsap_698,
Loxodonta africana	ENSLAFG00000003752	1 retrocopy	retro_lafr_668,
Pongo abelii	ENSPPYG00000015694	3 retrocopies	retro_pabe_527, retro_pabe_545, retro_pabe_640,
Pan troglodytes	ENSPTRG00000017146	2 retrocopies	retro_ptro_444, retro_ptro_487,