RetrogeneDB ID: retro_mdom_1584

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:51500875..51501336(+)
• Located in intron of: ENSMODG00000025137

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013383
• Aliases: None
• Description: None

Sequence

>retro_mdom_1584
ACCCCTGTTTGCTGTGTACTTTGGATTGGAGGGGAGAAATCACACCAGAAGAACCCAGATAATATATTGAATTATCCCCA
GCTCTTTGCAGCTGGGATGTTATCTGGTGCATTCATAAGAGGAAACATGACTCCTGGAGCAAGAATCAAACATCTACTAT
GGAGCCACGTCTCTTCAGGAGGAAAAAAAAAATACATTGATGCTTTGGACTGTGCCCAAAAAATTGTATCAGGAAAATGG
AATAAGAGGCATTTACAAAGGAATTATGCTTACTAACTACATGCAAGATGTTCCTGCCAGACGAATGTATTTCATGACTT
ATGAGCAGTAAAATATCTCTTCAACCCAGAAGGAGAAAATGTTAGTGCCCTTGAATCCTGAATCCTGATGGCTGGAGGCA
TCATAGGAACTTTAGCTGGGTTGTGACTGTCCCTCCAGATGTGCTGAAGTCCTACTTTCAG

Alignment

ORF - retro_mdom_1584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.63 %
• Parental protein coverage: 51.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TPMFAVCFFGFGLGKKLQQKNPDDVLTYPQLFAAGMLSGVFTTGIMTPGERIKCLLQIQASSG-ETKYTG
          TP...V...G...G.K..QKNPD..L.YPQLFAAGMLSG.F..G.MTPG.RIK.LL....SSG....Y..
Retrocopy TPVCCVLWIG---GEKSHQKNPDNILNYPQLFAAGMLSGAFIRGNMTPGARIKHLLWSHVSSGXXXXYID

Parental  ALDCA-KKVYQESGIRGIYKGTMLT-LLRDVPASGMYFMTYEW-LKNILTPEGKSVNELSVPQILFAGGA
          ALDCA.KK.YQE.GIRGIYKG.MLT....DVPA..MYFMTYE...K....PEG..V..L....IL.AGG.
Retrocopy ALDCA>KKLYQENGIRGIYKGIMLTNYMQDVPARRMYFMTYEQ<VKYLFNPEGENVSALE-S*ILMAGGI

Parental  AGI-FNWVVAIPPDVLKSRFQ
          .G..F.WVV..PPDVLKS.FQ
Retrocopy IGT<FSWVVTVPPDVLKSYFQ

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_1584 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1584 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
Callithrix jacchus	ENSCJAG00000003285	1 retrocopy	retro_cjac_2338,
Homo sapiens	ENSG00000178537	1 retrocopy	retro_hsap_3469,
Gorilla gorilla	ENSGGOG00000028046	1 retrocopy	retro_ggor_2341,
Macaca mulatta	ENSMMUG00000015418	1 retrocopy	retro_mmul_1764,
Monodelphis domestica	ENSMODG00000013383	3 retrocopies	retro_mdom_1584 , retro_mdom_229, retro_mdom_266,
Nomascus leucogenys	ENSNLEG00000006700	1 retrocopy	retro_nleu_342,
Pongo abelii	ENSPPYG00000013892	1 retrocopy	retro_pabe_2865,
Pan troglodytes	ENSPTRG00000014900	1 retrocopy	retro_ptro_2352,
Drosophila melanogaster	FBgn0031881	1 retrocopy	retro_dmel_15,