RetrogeneDB ID: retro_mdom_257

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:379823911..379824772(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000029561
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009978
• Aliases: None
• Description: None

Sequence

>retro_mdom_257
AGAGGAGTAGAACATGGTCCTTCAGCCATAAGAAAGGCAGGGTTATTGAAATGGCTCTCCAACTTGGGTTGCTGGGTGAA
TGACTTGGGAAATCTGAGTTTTACCCCTGTGGCCAGTGATGAGTGCTACAACAACCTAATTGTGAATCCTTACTCATTGG
GCCTTGCCAACCAAGAATTGGCTGAGGCAGTTAGCAGGGCTGTCTCTTCTGGTCACTGCTGCATCACTGTGGGAGGAGAC
CACAGTTTGGCAATTGGTTCCATTAGTGGCCATGTTCAGCACTGCCCAGACTTGTGTGTTATCTGGGTTGACGTTCACGC
TGATATCAACACACCCCTTACCACTTTGTCAGGGAGTCTGCACGGACAATCAGTCTCCTTCCTCCTTAGAGAACTACAGG
ACAAGGTACCATCTCTCCCAGCATTCTCTTGGATCAAGCCCTGTCTCTCATCCCCAGATATTGTGAATATTTCCCTAAGA
GATGTGGATCCTGCTGAACATTTTATTCTAAAAAATCATGATATTTTGTACTTTTCAATAAGAGATATTGATCGTCTTGG
AATCCAGAATGTCATGGAACAGACATTTGATCAACTGATCAGCAAAAAAAAACAAAGACCAATTCATCTGAGCTTTGACA
TTGATGCTTTTGGCCCTTCACTGGCTCCAGCAACAGGGACTCCTATTGTAGGTGGGCTGACTTATCGGGAAGGCATGTAC
ATTACAGAGGAGATACATAATACAGGTTTGCTGTCAGCCCTGGATCTAGTTGAGGTCAATCCTCTCTTGGCTACTTCAGA
GGAGGATGTGAAGGCCACAGCTGGACTAGCTGTGGTTGTGATTGCCTCAAGCTTTGGCTAG

Alignment

ORF - retro_mdom_257 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.66 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGVEHGPSAIREAGLLKRLSNLGCRVNDLGDLSFTPVASDECYNNLIVNPRSVGLANQELAEAVSRAVSS
          RGVEHGPSAIR.AGLLK.LSNLGC.VNDLG.LSFTPVASDECYNNLIVNP.S.GLANQELAEAVSRAVSS
Retrocopy RGVEHGPSAIRKAGLLKWLSNLGCWVNDLGNLSFTPVASDECYNNLIVNPYSLGLANQELAEAVSRAVSS

Parental  GHRCITVGGDHSLAIGSISGHVRHCPDLCVIWVDAHADINTPLTTLSGSLHGQPVSFLLRELQDKVPSLP
          GH.CITVGGDHSLAIGSISGHV.HCPDLCVIWVD.HADINTPLTTLSGSLHGQ.VSFLLRELQDKVPSLP
Retrocopy GHCCITVGGDHSLAIGSISGHVQHCPDLCVIWVDVHADINTPLTTLSGSLHGQSVSFLLRELQDKVPSLP

Parental  GFSWIKPCLSSPDIVYIGLRDVDPAEHFILKNYDILYFSMRDIDRLGIQKVMEQTFDQLIS-KKQRPIHL
          .FSWIKPCLSSPDIV.I.LRDVDPAEHFILKN.DILYFS.RDIDRLGIQ.VMEQTFDQLIS.KKQRPIHL
Retrocopy AFSWIKPCLSSPDIVNISLRDVDPAEHFILKNHDILYFSIRDIDRLGIQNVMEQTFDQLISKKKQRPIHL

Parental  SFDIDAFDPSLAPATGTPVVGGLTYREGMYITEEVHNTGLLSALDLVEVNPLLATSEEDVKATAGLAVDV
          SFDIDAF.PSLAPATGTP.VGGLTYREGMYITEE.HNTGLLSALDLVEVNPLLATSEEDVKATAGLAV.V
Retrocopy SFDIDAFGPSLAPATGTPIVGGLTYREGMYITEEIHNTGLLSALDLVEVNPLLATSEEDVKATAGLAVVV

Parental  IASSFG
          IASSFG
Retrocopy IASSFG

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	54.95 RPM
SRP007412_cerebellum	0.00 RPM	86.18 RPM
SRP007412_heart	0.00 RPM	28.91 RPM
SRP007412_kidney	0.00 RPM	603.11 RPM
SRP007412_liver	0.00 RPM	39.27 RPM
SRP007412_testis	0.00 RPM	310.17 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_257 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_257 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005722	1 retrocopy	retro_acar_91,
Choloepus hoffmanni	ENSCHOG00000007159	1 retrocopy	retro_chof_1179,
Callithrix jacchus	ENSCJAG00000015277	4 retrocopies	retro_cjac_1933, retro_cjac_2357, retro_cjac_2561, retro_cjac_902,
Dasypus novemcinctus	ENSDNOG00000004808	1 retrocopy	retro_dnov_251,
Homo sapiens	ENSG00000081181	1 retrocopy	retro_hsap_3501,
Gorilla gorilla	ENSGGOG00000005615	1 retrocopy	retro_ggor_2367,
Microcebus murinus	ENSMICG00000010837	1 retrocopy	retro_mmur_874,
Monodelphis domestica	ENSMODG00000009978	1 retrocopy	retro_mdom_257 ,
Monodelphis domestica	ENSMODG00000017584	1 retrocopy	retro_mdom_1318,
Nomascus leucogenys	ENSNLEG00000000741	2 retrocopies	retro_nleu_2875, retro_nleu_792,
Oryctolagus cuniculus	ENSOCUG00000000584	1 retrocopy	retro_ocun_277,
Pongo abelii	ENSPPYG00000005926	1 retrocopy	retro_pabe_2893,
Pan troglodytes	ENSPTRG00000006467	1 retrocopy	retro_ptro_2373,