RetrogeneDB ID: retro_mdom_1166

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:330998458..330999016(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010489
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLIC1
• Ensembl ID: ENSMODG00000015240
• Aliases: None
• Description: chloride intracellular channel 1 [Source:HGNC Symbol;Acc:2062]

Sequence

>retro_mdom_1166
AGGAGAACAGAGAGAGTGCAGAAGTTGCATCCTGGAGGTCAGCTCCCATTTTTACTGTATGCACAGAAGTGCACATGGAC
ACTACTAAGATTGAAGAGTTTCTGGAGGCGATGCTGAGCCTCTTCTAGGTACCTGAAGTTGGCAGTTAAGAACCCAGAAT
CCAACACAGCTAGCTTGGATGTCTTTGCCAAATTTCCTGCCTGTATCAAGAATTCAAACCGAGCGCTCAATGCCAACTTG
GAAGCCCTAAAGGTTCTGGACAACTATCTGACATCACCACGTCCTAAGGAAATTGATGAAACAAGTGCAGAAGATGAGGG
TGTCTCCCACAGATTTCTGGATGGTGATGAACTCACATTGGCTGATTGCAACCTGCTGCCCAAGCTTCACATTGTACAGG
TTGTATGTAAGAAATATTGGGGATTTTCTATCCCAGAAGAATTCTGAGGGTTGCAAAGATACCTGCCTAATGTTTATGCT
AGAGAAGAGTTTATCTCTACTTGTACAGATGCAGAGTAGATAGAGCTGGCCTATGAGCTAGTAGACAAAGCCCTAAAG

Alignment

ORF - retro_mdom_1166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.96 %
• Parental protein coverage: 79.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRTETVQKLCPGGQLPFLLYG-TEVHTDTNKIEEFLEAVLS-PPRYPKLAAKNPESNTAGLDVFAKFSAY
          RRTE.VQKL.PGGQLPFLLY..TEVH.DT.KIEEFLEA.LS...RY.KLA.KNPESNTA.LDVFAKF.A.
Retrocopy RRTERVQKLHPGGQLPFLLYA<TEVHMDTTKIEEFLEAMLS>SSRYLKLAVKNPESNTASLDVFAKFPAC

Parental  IKNSNPALNANLEKGLLKALKVLDNYLISPLPEEIDETSAEDEGVSHRKFLDGDELTLADCNLLPKLHIV
          IKNSN.ALNANLE...LK.L...DNYL.SP.P.EIDETSAEDEGVSHR.FLDGDELTLADCNLLPKLHIV
Retrocopy IKNSNRALNANLE--ALKVL---DNYLTSPRPKEIDETSAEDEGVSHR-FLDGDELTLADCNLLPKLHIV

Parental  QVVCKKYRGFSIPEEFRGLQRYLRNAYAREEFASTCPDAEEIELAYELVAKALK
          QVVCKKY.GFSIPEEF.GLQRYL.N.YAREEF.STC.DAE.IELAYELV.KALK
Retrocopy QVVCKKYWGFSIPEEF*GLQRYLPNVYAREEFISTCTDAE*IELAYELVDKALK

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
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1166 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1166 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 17 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000621	2 retrocopies	retro_cfam_481, retro_cfam_525,
Callithrix jacchus	ENSCJAG00000002788	1 retrocopy	retro_cjac_2972,
Dipodomys ordii	ENSDORG00000016424	3 retrocopies	retro_dord_506, retro_dord_524, retro_dord_550,
Felis catus	ENSFCAG00000019049	1 retrocopy	retro_fcat_1301,
Gorilla gorilla	ENSGGOG00000011331	1 retrocopy	retro_ggor_2153,
Macropus eugenii	ENSMEUG00000015201	1 retrocopy	retro_meug_254,
Macaca mulatta	ENSMMUG00000029827	3 retrocopies	retro_mmul_1269, retro_mmul_290, retro_mmul_902,
Monodelphis domestica	ENSMODG00000015240	1 retrocopy	retro_mdom_1166 ,
Monodelphis domestica	ENSMODG00000017298	1 retrocopy	retro_mdom_1408,
Nomascus leucogenys	ENSNLEG00000006264	3 retrocopies	retro_nleu_1296, retro_nleu_24, retro_nleu_2894,
Oryctolagus cuniculus	ENSOCUG00000022545	1 retrocopy	retro_ocun_1449,
Otolemur garnettii	ENSOGAG00000031840	4 retrocopies	retro_ogar_2402, retro_ogar_3273, retro_ogar_407, retro_ogar_982,
Procavia capensis	ENSPCAG00000013268	1 retrocopy	retro_pcap_30,
Pongo abelii	ENSPPYG00000016456	2 retrocopies	retro_pabe_1514, retro_pabe_886,
Pan troglodytes	ENSPTRG00000017982	2 retrocopies	retro_ptro_1238, retro_ptro_724,
Sarcophilus harrisii	ENSSHAG00000006493	1 retrocopy	retro_shar_28,
Tarsius syrichta	ENSTSYG00000001540	2 retrocopies	retro_tsyr_1452, retro_tsyr_722,