RetrogeneDB ID: retro_cpor_658

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_21:20568011..20568898(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3A3
• Ensembl ID: ENSCPOG00000008660
• Aliases: None
• Description: None

Sequence

>retro_cpor_658
AAAGATCAGAATGAACTTCTTGGGATGATACAGACCGAATCTGAGAAGAGATGAGAGAACCATACCTTTCCCGGATGGCC
AAAAGAGGCCAGCAGTGCAGTGACCCATGCTGGCCTCTGTCTCAATTTGTCTGCATTTGCCTCCTGGGAGGAGCTGGCCT
TTCTGGGGCTAGAAAGATGGAAGTCTGCACTCTTAGTTTTAGACCTGAAATGCCAGGGACCCTTGAAGAGCCAGACCAGA
AGATGTCTAGCACCAAAGTGAAGATCTTGGTATCACTGGATGACTCCCTGTTTGCCAAAACTCCCAAAGCAAAGGGCACT
AAGAGAGACCCTGAGAGGAACAAAGACATTGCTTTCCTAGAAGCCCAGATCTATGAATATGTTGAGATTCTTGGGGAACA
GCGACAGCTCACCCGTGAAAATGTGCAACACAAACAAGATGGGACAGGAGAAGAGCAAGAAGAGGAGGGGGAAGAGCCCA
TCAGTGAGAGTGAAAGTGGAGGTGAAGAGAATGAGATCATTACAACCCCCAAAACCTAGCCCTGGAGGGGATGGCAAGCC
CATCCTGTACTGGCTGTGTAAGCTACACTGCCTAAACATCAAGTACAATTGTGAGATTTGTGGGAGCCACACCTACCGAG
GCCGAAGGCCTTCCAGCAGCACCTCACTGAATGCATCATGTTTACTGCAGGTGGTGTTTGGGCGCTCGGAACACTGCTCA
CTTTGCTAATGTGACACAGATTGAAGATGCTGTCCCCTGTGGGCCAGGCTGAAACTGCAGAAGGCTTCAGAATGATGGCA
GCCTGACACTGAGGAAGAGTATGAAGACTCCAGAGGGAATGTTATAAAAAGAAAACCTATGAAGTTCTGAAAAGACAAGG
ACTGCTG

Alignment

ORF - retro_cpor_658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.08 %
• Parental protein coverage: 59.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  QDQNELFGKIQNEFEKKWENGTFPGWPKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLK
          .DQNEL.G.IQ.E.EK..EN.TFPGWPKE.SSA.THAG..L.LSAF.SWEELA.LGL.R.KSALL.L.LK
Retrocopy KDQNELLGMIQTESEKR*ENHTFPGWPKEASSAVTHAGLCLNLSAFASWEELAFLGLERWKSALLVLDLK

Parental  CGG-TLEERAQRLFSTKGKSLESLDTSLFAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRQLTH
          C.G.TLEE..Q...STK.K.L.SLD.SLFAK.PK.KGTKRD.ERNKDIAFLEAQIYEYVEILGEQRQLT.
Retrocopy CQG<TLEEPDQKMSSTKVKILVSLDDSLFAKTPKAKGTKRDPERNKDIAFLEAQIYEYVEILGEQRQLTR

Parental  ENVQRKQARTGEEREEEEEEQISESESEDEENEII-YNPKNLPL-GWDGKPIPYWLYKLHGLNINYNCEI
          ENVQ.KQ..TGEE.EEE.EE.ISESES..EENEII.YNP.NL.L.G.DGKPI.YWL.KLH.LNI.YNCEI
Retrocopy ENVQHKQDGTGEEQEEEGEEPISESESGGEENEII<YNPQNLAL<GGDGKPILYWLCKLHCLNIKYNCEI

Parental  CGNYTYRG-PKAFQRHFAE-WRHAHGMRCLGIPNTAHFANVTQIEDAV-SLWAKLKLQKASERWQPDTEE
          CG..TYRG.PKAFQ.H..E...H.....CLG..NTAHFANVTQIEDAV..LWA.LKLQKASE.WQPDTEE
Retrocopy CGSHTYRG<PKAFQQHLTE<MHHVYCRWCLGARNTAHFANVTQIEDAV<PLWARLKLQKASE*WQPDTEE

Parental  EYEDSSGNVV-NKKTYEDLKRQGLL
          EYEDS.GNV...KKTYE.LKRQGLL
Retrocopy EYEDSRGNVI<KKKTYEVLKRQGLL

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	32.04 RPM
SRP017611_kidney	0.00 RPM	43.55 RPM
SRP017611_liver	0.00 RPM	32.17 RPM
SRP040447_lung	0.03 RPM	43.99 RPM
SRP040447_skeletal_muscle	0.00 RPM	17.74 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_658 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_658 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001262	1 retrocopy	retro_amel_485,
Canis familiaris	ENSCAFG00000003222	1 retrocopy	retro_cfam_176,
Callithrix jacchus	ENSCJAG00000002176	1 retrocopy	retro_cjac_4109,
Cavia porcellus	ENSCPOG00000008660	1 retrocopy	retro_cpor_658 ,
Homo sapiens	ENSG00000183431	2 retrocopies	retro_hsap_2441, retro_hsap_937,
Macropus eugenii	ENSMEUG00000002534	3 retrocopies	retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta	ENSMMUG00000023199	1 retrocopy	retro_mmul_631,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269,
Nomascus leucogenys	ENSNLEG00000011720	1 retrocopy	retro_nleu_2775,
Pan troglodytes	ENSPTRG00000000559	2 retrocopies	retro_ptro_1411, retro_ptro_649,
Sorex araneus	ENSSARG00000014204	1 retrocopy	retro_sara_407,