RetrogeneDB ID: retro_cpor_249

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_11:31271894..31272383(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL2BP
• Ensembl ID: ENSCPOG00000011406
• Aliases: None
• Description: None

Sequence

>retro_cpor_249
ATCGATGCTCTGGAGTAGGAGAAATTGGCCCTGTCCTTCTCCTCTGCCTATGACGGAAAATTGGATGCTGTGATTGGATA
CTTGGAGGACGTTATCATGAATGATGGGTTCCAGTTTTACAGAGAAATTTCATGGACAAGTACTACCAGGAATTTGAAGA
TACAGAGGAGAATAAACTCACCTACACCCTCATCTTTCAAAGCATATATTGCTCTAGTCAAAAAATACACTGAGGAGCAG
TTCCTGATGTGGATCCCAGAGTTCAGCATGGTGGCCTTCGCAGCATTGCTACAGCAGCACCATAAAAAGGAAGGGGCTGG
TGCCATCTTTGACATACTGCGCACGCTTATAGATTTTTCTGGCTTTTAAAGAAATGTTTTTGGTCGACAGAGCAGAAAAG
GAAGCCCAGGGGCTGGATTTAAAAAGTGGCTGAGTGTGACATCATTGTGCAAATCCTCTCCTGTGCCAGCTTCCCAGAAT
AATCTGCGT

Alignment

ORF - retro_cpor_249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.65 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDALEEENLALSFSSASDAEFDAVVGYLEDIIMDDEFQ-LLQRNFMDKYYQEFEDTEENKLTYTPIFNE-
          .DALE.E.LALSFSSA.D...DAV.GYLED.IM.D.FQ..LQRNFMDKYYQEFEDTEENKLTYT.IF...
Retrocopy IDALE*EKLALSFSSAYDGKLDAVIGYLEDVIMNDGFQ<VLQRNFMDKYYQEFEDTEENKLTYTLIFQS>

Parental  YISLVEKYIEEQLLERIPGFSMAAFTTTLQ-HHKDEVAGDIFDMLLTFTDF-LAFKEMFLDYRAEKEGRG
          YI.LV.KY.EEQ.L..IP.FSM.AF...LQ.HHK.E.AG.IFD.L.T..DF.LAFKEMFL..RAEKE..G
Retrocopy YIALVKKYTEEQFLMWIPEFSMVAFAALLQQHHKKEGAGAIFDILRTLIDF>LAFKEMFLVDRAEKEAQG

Parental  LDLSSG-LVVTSLCKSSPVPASQNNLR
          LDL.SG.L.VTSLCKSSPVPASQNNLR
Retrocopy LDLKSG<LSVTSLCKSSPVPASQNNLR

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	28.64 RPM
SRP017611_kidney	0.00 RPM	13.09 RPM
SRP017611_liver	0.00 RPM	8.57 RPM
SRP040447_lung	0.00 RPM	17.23 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.40 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_249 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_249 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 21 parental genes, and 91 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012116	9 retrocopies	retro_cjac_1766, retro_cjac_1920, retro_cjac_1928, retro_cjac_2548, retro_cjac_2580, retro_cjac_2698, retro_cjac_4074, retro_cjac_625, retro_cjac_689,
Cavia porcellus	ENSCPOG00000011406	5 retrocopies	retro_cpor_1501, retro_cpor_203, retro_cpor_249 , retro_cpor_299, retro_cpor_571,
Equus caballus	ENSECAG00000016621	3 retrocopies	retro_ecab_307, retro_ecab_344, retro_ecab_754,
Felis catus	ENSFCAG00000002937	3 retrocopies	retro_fcat_400, retro_fcat_69, retro_fcat_974,
Homo sapiens	ENSG00000102931	7 retrocopies	retro_hsap_1189, retro_hsap_1846, retro_hsap_3237, retro_hsap_3263, retro_hsap_3270, retro_hsap_4293, retro_hsap_999,
Gorilla gorilla	ENSGGOG00000005471	5 retrocopies	retro_ggor_2159, retro_ggor_2202, retro_ggor_2222, retro_ggor_2868, retro_ggor_927,
Loxodonta africana	ENSLAFG00000008633	3 retrocopies	retro_lafr_103, retro_lafr_228, retro_lafr_418,
Microcebus murinus	ENSMICG00000012467	6 retrocopies	retro_mmur_1066, retro_mmur_1385, retro_mmur_1444, retro_mmur_1515, retro_mmur_247, retro_mmur_499,
Myotis lucifugus	ENSMLUG00000012680	3 retrocopies	retro_mluc_1338, retro_mluc_1843, retro_mluc_746,
Macaca mulatta	ENSMMUG00000020352	7 retrocopies	retro_mmul_1260, retro_mmul_2037, retro_mmul_2055, retro_mmul_2059, retro_mmul_223, retro_mmul_2232, retro_mmul_2458,
Monodelphis domestica	ENSMODG00000013511	1 retrocopy	retro_mdom_1182,
Nomascus leucogenys	ENSNLEG00000002803	7 retrocopies	retro_nleu_1050, retro_nleu_1939, retro_nleu_1946, retro_nleu_2114, retro_nleu_2332, retro_nleu_2428, retro_nleu_955,
Oryctolagus cuniculus	ENSOCUG00000000582	1 retrocopy	retro_ocun_431,
Ochotona princeps	ENSOPRG00000006931	2 retrocopies	retro_opri_675, retro_opri_98,
Pongo abelii	ENSPPYG00000007384	8 retrocopies	retro_pabe_1318, retro_pabe_1348, retro_pabe_1453, retro_pabe_2684, retro_pabe_2704, retro_pabe_3498, retro_pabe_843, retro_pabe_990,
Pan troglodytes	ENSPTRG00000008150	7 retrocopies	retro_ptro_1231, retro_ptro_2189, retro_ptro_2207, retro_ptro_2910, retro_ptro_2948, retro_ptro_752, retro_ptro_816,
Rattus norvegicus	ENSRNOG00000016991	1 retrocopy	retro_rnor_780,
Sorex araneus	ENSSARG00000005442	1 retrocopy	retro_sara_190,
Ictidomys tridecemlineatus	ENSSTOG00000010254	1 retrocopy	retro_itri_638,
Tupaia belangeri	ENSTBEG00000014441	1 retrocopy	retro_tbel_2991,
Tarsius syrichta	ENSTSYG00000004923	10 retrocopies	retro_tsyr_1003, retro_tsyr_1066, retro_tsyr_1205, retro_tsyr_1728, retro_tsyr_1755, retro_tsyr_1958, retro_tsyr_2144, retro_tsyr_28, retro_tsyr_298, retro_tsyr_351,