RetrogeneDB ID: retro_cpor_845

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:7127516..7128249(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT2
• Ensembl ID: ENSCPOG00000013687
• Aliases: None
• Description: None

Sequence

>retro_cpor_845
ACCACCATCTCCTATGTTGATGAGCAGTTTGAACGCTACCTGCATGATGAGAGTGGCTTAAACAGGCGCCACATCATTGA
CAACAGGGTGCACTGCTGCTTCTACTTCATTTCACCTTTGGACATGCACTGAAGCCTTCAGATGTTGCATTTATGAACAC
AATACACAACAAGGTAAACATTATGCCTGTCATTGCGAAAGCTGACACTCTCACTCTGGAGGAGCATGAGTGACTGAAGA
AAAGAATTCTGGATGAAATTGAAGAACATAACATCAAAAACTATCACTTATCTGATGCAGAATCACATGAAGATGAAGAC
TTTAAAGAGCAGACTAGGCTTCTCAAGGCCAGTATCCCATTCTCTGTGGTGGGATCCAACCAGTTGATGGAAGCCAAAGG
CAAGAAGTTCAGAGGTTGCCTCTATTCATCGGGTGTTGTGGAGGTGGAGAACCCAGAACATAATGATTTTCTGAAGCTAA
GAACGATGCTTATTACACACATGCAAGATCTATAGGAAGTGACTCAGGACCTTTACTATGAAGCTTTCATTCTGAGAGGC
TTAAGAGAGGTGACAGGAAAGTAGAAAATGAGGATATGAATAAAGATCAGACCCTGCTGGAAAAGGAAGTGGAACTCCAC
AGCATGCAAGAGATGATCTCAAGGATGCAGGCACAGATGCAGATGCAGATGCAGGATGGTGATGGTGACAGTGGAGCTCT
TGGGCACCATGTG

Alignment

ORF - retro_cpor_845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 67.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TIISYIDEQFERYLHDESGLNRRHIIDNRVHCCFYFISP-FGHGLKPLDVAFMKAIHNKVNIVPVIAKAD
          T.ISY.DEQFERYLHDESGLNRRHIIDNRVHCCFYFISP.FGH.LKP.DVAFM..IHNKVNI.PVIAKAD
Retrocopy TTISYVDEQFERYLHDESGLNRRHIIDNRVHCCFYFISP<FGHALKPSDVAFMNTIHNKVNIMPVIAKAD

Parental  TLTLKERERLKKRILDEIEEHNIKIYHLPDAESDEDEDFKEQTRLLKASIPFSVVGSNQLIEAKGKKVRG
          TLTL.E.E.LKKRILDEIEEHNIK.YHL.DAES.EDEDFKEQTRLLKASIPFSVVGSNQL.EAKGKK.RG
Retrocopy TLTLEEHE*LKKRILDEIEEHNIKNYHLSDAESHEDEDFKEQTRLLKASIPFSVVGSNQLMEAKGKKFRG

Parental  RLYPWGVVEVENPEHNDFLKLRTMLITHMQDLQEVTQDLHYE-NFRSERLKRGGRKVENEDMNKDQILLE
          .LY..GVVEVENPEHNDFLKLRTMLITHMQDL.EVTQDL.YE..F.SERLKRG.RKVENEDMNKDQ.LLE
Retrocopy CLYSSGVVEVENPEHNDFLKLRTMLITHMQDL*EVTQDLYYE<SFHSERLKRGDRKVENEDMNKDQTLLE

Parental  KEAELRRMQEMIARMQAQMQLQMQGGDGDSGALGHHV
          KE.EL..MQEMI.RMQA........GDGDSGALGHHV
Retrocopy KEVELHSMQEMISRMQAXXXXXXXDGDGDSGALGHHV

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	38.59 RPM
SRP017611_kidney	0.00 RPM	49.41 RPM
SRP017611_liver	0.00 RPM	27.03 RPM
SRP040447_lung	0.05 RPM	99.87 RPM
SRP040447_skeletal_muscle	0.00 RPM	39.21 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_845 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_845 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002608	1 retrocopy	retro_btau_1185,
Canis familiaris	ENSCAFG00000012960	1 retrocopy	retro_cfam_1477,
Choloepus hoffmanni	ENSCHOG00000008715	5 retrocopies	retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Callithrix jacchus	ENSCJAG00000006122	1 retrocopy	retro_cjac_1501,
Cavia porcellus	ENSCPOG00000013687	1 retrocopy	retro_cpor_845 ,
Loxodonta africana	ENSLAFG00000011964	1 retrocopy	retro_lafr_4,
Macropus eugenii	ENSMEUG00000016519	1 retrocopy	retro_meug_39,
Myotis lucifugus	ENSMLUG00000007108	1 retrocopy	retro_mluc_1594,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Mustela putorius furo	ENSMPUG00000000166	1 retrocopy	retro_mputfur_436,
Nomascus leucogenys	ENSNLEG00000013873	1 retrocopy	retro_nleu_1848,
Otolemur garnettii	ENSOGAG00000004457	1 retrocopy	retro_ogar_2239,
Pteropus vampyrus	ENSPVAG00000000558	1 retrocopy	retro_pvam_448,
Rattus norvegicus	ENSRNOG00000017952	1 retrocopy	retro_rnor_1110,
Ictidomys tridecemlineatus	ENSSTOG00000013357	1 retrocopy	retro_itri_1227,
Drosophila melanogaster	FBgn0011710	1 retrocopy	retro_dmel_35,