RetrogeneDB ID: retro_cpor_824

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:16455481..16456457(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000026447
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ERGIC2
• Ensembl ID: ENSCPOG00000015668
• Aliases: None
• Description: None

Sequence

>retro_cpor_824
ATGAGGCGACTGAATCGGAAGAAAATCTTAAATTTGGTGAAAGAGCTAGATGCCTGTCCTCAGAGCTATGTGGAGACTTC
AGTGGGGATAGTTTCTCTAATAGCATTTACACACAATGGCTTTATTAATGGAATTCTCAGTATATCAAGACACATGGATA
AAGTATAATATGAAGTAGACAAGGATTTTTCTAGTAAACTGAGAATCGACATAGATATCACTGTTGCCATGAAGTGCCAG
TATGTTGGAGCAGACGTACTGGGTTTAGCAGAAACCATGGTTGCATCTGCAGATGGTCTAACTTATGAACCAGCAATGTC
TGATCTTTCACCACAGCAGAAAGAGTGGCAGCGGATGCTGCAGCTGATTCAGAGCAGACTTCAAGAAGAGCATTCTCTTC
AAGATGTGATATTTAAAAGTGCTTTTAAAAGTGCATCAACAGCACTTGCACCAAGGGGAGACAATTCATCGCAGTGGCGG
ATGCAGGCCGAATTCGTGGTTACCTCTATGTTAATAAAGTAACCAGGCATTTTCACCTAACGGTGGGCCAGGCAATTCCA
CATCCTCGGGTCACGCACACTTGGGAGCACTTGGCAACCATGACTCTTACAACTTTTCTCACGGAATAATTCATTTATCT
TTTGGAGAACTTGTTCCAGGAATCATTAATCCTTTAGATGGAACTGAAAAAATTGCCGTAGATCACAACCAGATGTTCCA
ATATTTTATTACAGTTGTGTCAACAAAATTACATACATACAAAATTTCAGCAGACACACATCAGTTTTCTGTGACAGAAA
GGGAGCGAATCATCAACCGTGCTGCAGGCAGCTATGGGGTCTCGGGGATATTTATGAAGTATAACCTCAGTTTTCTTACG
ATGACAGTGACTGAGGAGCACGTGCCATTCTGGCAGGTTTTTGTCTGTGGTATTGTTGGAGGAATGTTCTCTACAACAGG
CATGTTGCATGGAATA

Alignment

ORF - retro_cpor_824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.12 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MRRLNRKKTLNLVKELDAFPKVPQSYVETSASGGTAVSLIAFT-TMALLTIMEFSVYQDTWMKYE-YEVD
          MRRLNRKK.LNLVKELDA....PQSYVETS......VSLIAFT.TMALL..MEFSVYQDTW.KY..YEVD
Retrocopy MRRLNRKKILNLVKELDA---CPQSYVETSVG---IVSLIAFT>TMALL--MEFSVYQDTWIKYN<YEVD

Parental  KDFSSKLRINIDITVAMKCQYVGADVLDVAETMVASADGLVYEPAIFDLSPQQKEWQRMLQLIQSRLQEE
          KDFSSKLRI.IDITVAMKCQYVGADVL..AETMVASADGL.YEPA..DLSPQQKEWQRMLQLIQSRLQEE
Retrocopy KDFSSKLRIDIDITVAMKCQYVGADVLGLAETMVASADGLTYEPAMSDLSPQQKEWQRMLQLIQSRLQEE

Parental  HSLQDVIFKSAFKSASTALPPREANSSQ-SPDACRIHGHLYVNKVAGNFHITVGKAIPHPR-GHAHLAAL
          HSLQDVIFKSAFKSASTAL.PR..NSSQ...DA.RI.G.LYVNKV...FH.TVG.AIPHPR.GHAHL.AL
Retrocopy HSLQDVIFKSAFKSASTALAPRGDNSSQ<VADAGRIRGYLYVNKVTRHFHLTVGQAIPHPR<GHAHLGAL

Parental  VNHDSYNFSHRIDHLSFGELVPGIINPLDGTEKIAVDHNQMFQYFITVVPTKLHTYKISADTHQFSVTER
          .NHDSYNFSH.I.HLSFGELVPGIINPLDGTEKIAVDHNQMFQYFITVV.TKLHTYKISADTHQFSVTER
Retrocopy GNHDSYNFSHGIIHLSFGELVPGIINPLDGTEKIAVDHNQMFQYFITVVSTKLHTYKISADTHQFSVTER

Parental  ERIINHAAGSHGVSGIFMKYDLSSLMVTVTEEHMPFWQFFVRLCGIVGGIFSTTGMLHGI
          ERIIN.AAGS.GVSGIFMKY.LS.L..TVTEEH.PFWQ.FV..CGIVGG.FSTTGMLHGI
Retrocopy ERIINRAAGSYGVSGIFMKYNLSFLTMTVTEEHVPFWQVFV--CGIVGGMFSTTGMLHGI

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	0.06 RPM	18.58 RPM
SRP017611_kidney	0.10 RPM	19.47 RPM
SRP017611_liver	0.00 RPM	34.86 RPM
SRP040447_lung	0.00 RPM	21.74 RPM
SRP040447_skeletal_muscle	0.01 RPM	23.93 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_824 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_824 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015668	1 retrocopy	retro_cpor_824 ,
Ornithorhynchus anatinus	ENSOANG00000010582	1 retrocopy	retro_oana_32,
Oryctolagus cuniculus	ENSOCUG00000017255	1 retrocopy	retro_ocun_1540,
Pongo abelii	ENSPPYG00000004390	1 retrocopy	retro_pabe_657,
Rattus norvegicus	ENSRNOG00000001852	1 retrocopy	retro_rnor_1557,
Sarcophilus harrisii	ENSSHAG00000004822	1 retrocopy	retro_shar_386,
Tupaia belangeri	ENSTBEG00000011223	1 retrocopy	retro_tbel_3783,