RetrogeneDB ID: retro_mdom_1148

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:252763334..252763780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLTA
• Ensembl ID: ENSMODG00000002610
• Aliases: None
• Description: clathrin, light chain A [Source:HGNC Symbol;Acc:2090]

Sequence

>retro_mdom_1148
GGCAGTGGCTAATCGGACCTCAGCAGCAATGAAGATGTGGACACCACTGCCTTCCTGGCTCATCAGGAGAACCACATTAC
AGGCATCTAGAAGGATAAAGAGCTTCAATATCCTGCACAACTGGGGTGTGCTTGCCTCCCTGCAAGGGGAGCCCCTTGAG
CCCCAGATGCTATTGATGGAGTGATGAATAGAGAATACTATCAGAAAAGTAATGGTCCAACAAGTAGTTATGCAGCTATA
TCACAAGTGGATCAATTAATGTCAGAACCTGAGAGTATTCCTAGAAGGAGAGAAGATCAAATGGAATGTCTGCAAGTCCT
TGATTCTTGGAATCAGGAAGCATAAAGGAAAGAAAAAAGCAATAAAAGAATTGGAAGAATGGTATGCAAGGCAATATGAA
CAACTACTAAACCCAAAGTGTATAACAGGCAGCTGAAGAAGCTTTT

Alignment

ORF - retro_mdom_1148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.82 %
• Parental protein coverage: 59.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GNGVASGGSSEEDPAAAFLAQQESEIAGIENDE-GFSILDTGSVPASLQGEP-PGGPDAIDAVMNGEYYQ
          G.G.....S.E.....AFLA.QE..I.GI..D...F.IL....V.ASLQGEP.P..PDAID.VMN.EYYQ
Retrocopy GSG*SDLSSNEDVDTTAFLAHQENHITGI*KDK>SFNILHNWGVLASLQGEP<P*APDAIDGVMNREYYQ

Parental  ESNGPTDSYAAISQVDRLQSEPESIRKWREEQMERLEVLDANSRKQEA-EWKEKAIKELEEWYARQDEQL
          .SNGPT.SYAAISQVD.L.SEPESI...RE.QME.L.VLD..S..QEA...K.KAIKELEEWYARQ.EQL
Retrocopy KSNGPTSSYAAISQVDQLMSEPESIPRRREDQMECLQVLD--SWNQEA>KGKKKAIKELEEWYARQYEQL

Parental  -QKTKVNNR-VADEAF
          ..K.KV.NR..A.EAF
Retrocopy <TKPKVYNR<AAEEAF

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_1148 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1148 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001137	1 retrocopy	retro_btau_327,
Homo sapiens	ENSG00000122705	2 retrocopies	retro_hsap_4022, retro_hsap_955,
Macropus eugenii	ENSMEUG00000010858	1 retrocopy	retro_meug_480,
Macaca mulatta	ENSMMUG00000006132	2 retrocopies	retro_mmul_2319, retro_mmul_785,
Monodelphis domestica	ENSMODG00000002610	1 retrocopy	retro_mdom_1148 ,
Monodelphis domestica	ENSMODG00000005190	1 retrocopy	retro_mdom_1495,
Nomascus leucogenys	ENSNLEG00000003874	1 retrocopy	retro_nleu_659,
Pongo abelii	ENSPPYG00000019069	1 retrocopy	retro_pabe_3300,
Pan troglodytes	ENSPTRG00000020930	1 retrocopy	retro_ptro_2727,