RetrogeneDB ID: retro_cpor_987

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:1345600..1346299(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIN
• Ensembl ID: ENSCPOG00000010515
• Aliases: None
• Description: None

Sequence

>retro_cpor_987
AGAAGAACCCAGGACCTCGAGGATGAAGAAAAGACTGCCACATTGATTGCAGAACAGGTGCCAAGGGGTCTGCAAAGGAA
GGAGCAGGAGGCCCCTGTGTGTACAGAATTAAGCAGAGAAAGCGATGAAGAGAAAGTTACACTTCATGTGAATTGAGGAG
CAGGTATTTCAGCAGGAGCAACGGCGTCCCGATCCAATTGTTTGGGGTCCAGCGCACTGACGATGCTGGGGAGAATGGCC
TCAGTGAAAGGAAAAGAACCTTCCCAGAGCTCGGCTCAGGCTAAGGAAAGGAAAAGGAGGCCTGCGCTTGAGGAACTCGT
GGCGATCGAAGAAGAGAAGAAAAGAACTTGGCGAACAGACTATTGGCTGCAGCCTGAAATCATTGTGAAAATCAAAACCA
AAAATCTTGGAGAGAAACACCATCAGGAAAGGGTGTGGCTAAGGGGGTCGTCGACAATTACACAGCCGCGTAAAGATCAG
CTCTGGAGACCAGCTGAAACCTGACCAGACTCCTTTAGAGACAGTCACTGCAGCACCGGGAAAAAGAATCCTGGTTTTCA
GTGGAGGTTACGGAGGAAATTCAGGCACCCTGGAATCATCAATGAAAAAACTTTTTCAACTACTATACTCCTTGAACCTG
GCCCTTTCAAAGGACGCAGAGTTGAAGGAATGCAGTATGAAGACATTTCTAAACTTGCC

Alignment

ORF - retro_cpor_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.87 %
• Parental protein coverage: 60.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKKQDLDDEEKTAKFIEEQVRRGLEGKEQEAPVFTELSRENDEEKVTFNLNKGACSSSGATTSKSSSLGP
          ...QDL.DEEKTA..I.EQV.RGL..KEQEAPV.TELSRE.DEEKVT...N.GA..S.GAT.S.S..LG.
Retrocopy RRTQDLEDEEKTATLIAEQVPRGLQRKEQEAPVCTELSRESDEEKVTLHVN*GAGISAGATASRSNCLGS

Parental  SALKTLGSTASVKRKETSQSSAQSKEKKKKKSALDEIMEIEEEKKRTSRTDYWLQPEIIVKIITKKLGEK
          SAL..LG..ASVK.KE.SQSSAQ.KE..K...AL.E...IEEEKKRT.RTDYWLQPEIIVKI.TK.LGEK
Retrocopy SALTMLGRMASVKGKEPSQSSAQAKE-RKRRPALEELVAIEEEKKRTWRTDYWLQPEIIVKIKTKNLGEK

Parental  YHKK-KGIVKEVIDRYTAV-VKMIDSGDKLKLDQTHLETVIPAPGKRILVLNGGYRGNEGTLES-INEKT
          .H...KG..K.V.D.YTA..VK.I.SGD.LK.DQT.LETV..APGKRILV..GGY.GN.GTLES.INEKT
Retrocopy HHQE<KGVAKGVVDNYTAA<VK-ISSGDQLKPDQTPLETVTAAPGKRILVFSGGYGGNSGTLES<INEKT

Parental  FSATIVIETGPLKGRRVEGIQYEDISKLA
          FS.TI..E.GP.KGRRVEG.QYEDISKLA
Retrocopy FSTTILLEPGPFKGRRVEGMQYEDISKLA

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	6.67 RPM
SRP017611_kidney	0.00 RPM	6.07 RPM
SRP017611_liver	0.00 RPM	3.92 RPM
SRP040447_lung	0.00 RPM	6.71 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.37 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_987 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_987 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004280	1 retrocopy	retro_acar_162,
Cavia porcellus	ENSCPOG00000010515	5 retrocopies	retro_cpor_279, retro_cpor_281, retro_cpor_818, retro_cpor_987 , retro_cpor_989,
Dipodomys ordii	ENSDORG00000003732	2 retrocopies	retro_dord_344, retro_dord_657,
Ficedula albicollis	ENSFALG00000001842	1 retrocopy	retro_falb_26,
Myotis lucifugus	ENSMLUG00000002261	1 retrocopy	retro_mluc_1186,
Rattus norvegicus	ENSRNOG00000026690	1 retrocopy	retro_rnor_2665,
Taeniopygia guttata	ENSTGUG00000002119	1 retrocopy	retro_tgut_9,