RetrogeneDB ID: retro_cpor_1034

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:21152156..21152864(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX8
• Ensembl ID: ENSCPOG00000002114
• Aliases: None
• Description: None

Sequence

>retro_cpor_1034
ATGGCACCAGACCTCTGGTTCAGCATATACGATTCCACCTGTCAGATTGCCTAGGAAATTACTGAGAAAATTCAACAATG
AAATCAGTATGAAAGAAAAGGCAAAAAGACATCCAAGCTTACCATGGCAATTCGAACTTTGCTGCTGAACTTGAAGAAAA
AGATTGCCCTTTTGGAGGATTTATTGCTAAGAGTGGTGTCAACACATCAAATAACACAACTGGAAGGAGATCAAAGACAG
AACCTACTAGATGATCTTGTAACTCAAGAGAGACTGCTTCTAGCATCCTTCAAGAACAAGTGTGCAGAGCCAGATCTAAT
CAGGCCCAGCCTGATGAGAAAAGAGGCTAAGTGAGGAACCCCCAACCCTTGGCTCTTTGAGGAGCTGGAGGAGATCAGAG
GCTTGGGATTTGATGAACTCTGGAAATTGCAGCAGAAAATTATCCAAAAACAAGACGCAAGCCTTGGTTCCCCTTCCCCT
ATCATAAGTTGCCAAAGACAAATGGGACAGGAAATTGAAAATGAGTTGGATGAACAAAGTAAGATAATTGATGACCTTGT
CAATCTTGTGGGGAACACAGATGAAAAGTTTCACACAGAAAACAGGCATATGACCTTGGTGGACAGAAAGTCAACTTCAT
GTGGGATGATAATGGTGATTTTATTGCTGCTTGTGGCTATTGTGGCCATTGCAGTCTGGCCAACCAAC

Alignment

ORF - retro_cpor_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.66 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPDPWFSTYDSTCQIAQDIAEKIQQRNQYERRGEKTPKLTVAIRTSLQNLKEKIALLKDLLLRAVSTHQ
          MAPD.WFS.YDSTCQIA..I.EKIQQ.NQYER.G.KT.KLT.AIRT.L.NLK.KIALL.DLLLR.VSTHQ
Retrocopy MAPDLWFSIYDSTCQIA*EITEKIQQ*NQYERKGKKTSKLTMAIRTLLLNLKKKIALLEDLLLRVVSTHQ

Parental  ITQLEGDRRQNLLDDLVTRERLLLASFKNEGAEPDLIRSSLMREEAKRGAPNPWLFEEPEETRGLGFDEL
          ITQLEGD.RQNLLDDLVT.ERLLLASFKN..AEPDLIR.SLMR.EAK.G.PNPWLFEE.EE.RGLGFDEL
Retrocopy ITQLEGDQRQNLLDDLVTQERLLLASFKNKCAEPDLIRPSLMRKEAK*GTPNPWLFEELEEIRGLGFDEL

Parental  RQQQQKIIQEQDAGLDALSSIISRQKQMGQEIGNELDEQNEIIDDLANLVENTDEKLRTETRRVTLVDRK
          ...QQKIIQ.QDA.L...S.IIS.Q.QMGQEI.NELDEQ..IIDDL.NLV.NTDEK..TE.R..TLVDRK
Retrocopy WKLQQKIIQKQDASLGSPSPIISCQRQMGQEIENELDEQSKIIDDLVNLVGNTDEKFHTENRHMTLVDRK

Parental  STSCGMIMVILLLLVAIVVVAVWPTN
          STSCGMIMVILLLLVAIV..AVWPTN
Retrocopy STSCGMIMVILLLLVAIVAIAVWPTN

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	7.82 RPM
SRP017611_kidney	0.00 RPM	17.90 RPM
SRP017611_liver	0.00 RPM	8.23 RPM
SRP040447_lung	0.00 RPM	18.69 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.16 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1034 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1034 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002045	1 retrocopy	retro_amel_911,
Canis familiaris	ENSCAFG00000017413	1 retrocopy	retro_cfam_1959,
Cavia porcellus	ENSCPOG00000002114	1 retrocopy	retro_cpor_1034 ,
Felis catus	ENSFCAG00000008276	1 retrocopy	retro_fcat_634,
Myotis lucifugus	ENSMLUG00000008612	1 retrocopy	retro_mluc_2329,
Mustela putorius furo	ENSMPUG00000007815	2 retrocopies	retro_mputfur_975, retro_mputfur_996,
Pteropus vampyrus	ENSPVAG00000001001	1 retrocopy	retro_pvam_147,
Rattus norvegicus	ENSRNOG00000003849	2 retrocopies	retro_rnor_2422, retro_rnor_2500,
Tarsius syrichta	ENSTSYG00000010795	1 retrocopy	retro_tsyr_1906,