RetrogeneDB ID: retro_cpor_1279

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_64:7870899..7871120(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSCPOG00000012143
• Aliases: None
• Description: None

Sequence

>retro_cpor_1279
GAACTCAAAATCATTGGACAGGATATCAGTAAGATTCACTCCAAAATGAAAATAACAGCACAGGTCAAGAAACTCAAAGA
AGCAGACTGTCAAAAACATGTAGTTCTAATGAACACACTCAGGGTTTTTTTGAAGGTCACAGAATTGCTAATAATCATAC
TCCAAAAGAAGTTTGAATAGAGGAAGAAAGTGTGATTGAAGTTTATCAGGAATCAGTGGGA

Alignment

ORF - retro_cpor_1279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.67 %
• Parental protein coverage: 76.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFL-FEGQRIADNHTPKELGMEEEDVIEVY
          .LK.IGQD.S.IH.K.K.T...KKLKE..CQ...V.MN.LR...FEG.RIA.NHTPKE...EEE.VIEVY
Retrocopy ELKIIGQDISKIHSKMKITAQVKKLKEADCQKHVVLMNTLRVF<FEGHRIANNHTPKEV*IEEESVIEVY

Parental  QEQTG
          QE..G
Retrocopy QESVG

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	16.68 RPM
SRP017611_kidney	0.00 RPM	27.11 RPM
SRP017611_liver	0.00 RPM	19.41 RPM
SRP040447_lung	0.00 RPM	21.21 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1279 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1279 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.

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Callithrix jacchus	ENSCJAG00000004961	3 retrocopies	retro_cjac_1686, retro_cjac_1932, retro_cjac_2610,
Cavia porcellus	ENSCPOG00000004581	9 retrocopies	retro_cpor_1029, retro_cpor_1297, retro_cpor_1496, retro_cpor_202, retro_cpor_357, retro_cpor_823, retro_cpor_838, retro_cpor_869, retro_cpor_894,
Cavia porcellus	ENSCPOG00000012143	1 retrocopy	retro_cpor_1279 ,
Cavia porcellus	ENSCPOG00000025203	3 retrocopies	retro_cpor_328, retro_cpor_645, retro_cpor_963,
Equus caballus	ENSECAG00000024693	4 retrocopies	retro_ecab_199, retro_ecab_365, retro_ecab_570, retro_ecab_935,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Homo sapiens	ENSG00000116030	5 retrocopies	retro_hsap_2007, retro_hsap_240, retro_hsap_2489, retro_hsap_262, retro_hsap_897,
Gorilla gorilla	ENSGGOG00000026439	5 retrocopies	retro_ggor_1451, retro_ggor_1550, retro_ggor_299, retro_ggor_311, retro_ggor_725,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Mustela putorius furo	ENSMPUG00000000335	2 retrocopies	retro_mputfur_257, retro_mputfur_33,
Mus musculus	ENSMUSG00000026021	5 retrocopies	retro_mmus_1594, retro_mmus_2129, retro_mmus_2135, retro_mmus_252, retro_mmus_2962,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Rattus norvegicus	ENSRNOG00000016133	2 retrocopies	retro_rnor_2015, retro_rnor_813,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,
Ictidomys tridecemlineatus	ENSSTOG00000025405	4 retrocopies	retro_itri_1193, retro_itri_1232, retro_itri_216, retro_itri_668,
Tursiops truncatus	ENSTTRG00000000642	4 retrocopies	retro_ttru_1646, retro_ttru_1652, retro_ttru_309, retro_ttru_399,