RetrogeneDB ID: retro_mdom_219

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:62410035..62410977(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025192
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011614
• Aliases: None
• Description: None

Sequence

>retro_mdom_219
ATGAAGCTCACAGATGGTGTTTTGCGGAGCTTCCGTGTAGCCAAGGTTTTCCGTGAGAACTCAGACAAAATCAACAGCTT
TGACTTCAGTGTCAGTGGTGAGACGGCTGTCTCAAGCAACAGTGACGATACCATCACTCTGTATGACTGTCAGGAGGGCA
AACCGAAGAGAACCCTGTACAGTAAGAAATATGGTGTAGACATAATTAAATACACACGGGCAGAAAGCACTGTAATATAT
AGCTGTAACAAAATAGATGATGCAATCCGATACCTGTCATTGCCTGAAAACAAATATATTAGATACTTCCATGGGCACAA
GAAAACCGTGGTGACCTTATCCATGTCACCCTCAGATGAAACCTTTATCTCTGGGTCTATAGATAAAACCATCCGACTCT
GGGATCTTCGATCTCCCAACTGCCAGGGTTTAATGCATCTCCAGGGAAAGCCAGTTTGTTCATTTGACCCAGAAGGGTTA
ATTTTTGCAGCTGGAGTCAATTCTGAAATGATTAAGCTTTATGATCTCCGCTCTTTTGATAAGGGTCCATTTGCAACCTT
CAGAATGGAGCAGGATAAGACCTATGAGTGGACGGGCTTAAAATTTAGCAAGGATGGCAAACACATCCTATTATATACCA
ATGGCAGCTGTTTCCATGTAGTTGATGCCTTTAAGGGTATAGTGACACATATTTTTTCAGGGTATAACAACCACCAGGCT
CTCTCATTGGAGGCTGCCTTCACTCCAGATTCTCAGTTTGTTATGATTGGGTCTGAAGATGGTAAGATCCATATCTGGAA
TGGAGAAAATGGAGAGAAAGTGGCTGTTTTGGATGCGAAACACACAGGTCCCATAACCTGCTTACAGTTCAATCCTAACT
TCATGACCTTTGCCAGTGCATGTTCTAACATGTCATTCTGGCTGCCTACTATTGATGATTAA

Alignment

ORF - retro_mdom_219 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLTDIVLRSFRVAKVFRENSDKINCFDFSPNGETVISSSDDDSIVLYDCQEGKPKRTLYSKKYGVDLIR
          MKLTD.VLRSFRVAKVFRENSDKIN.FDFS..GET..SS..DD.I.LYDCQEGKPKRTLYSKKYGVD.I.
Retrocopy MKLTDGVLRSFRVAKVFRENSDKINSFDFSVSGETAVSSNSDDTITLYDCQEGKPKRTLYSKKYGVDIIK

Parental  YTHAANTVVYSSNKIDDTIRYLSLHDNKYIRYFPGHNKRVVALSMSPIDDTFISGSLDKTIRLWDLRSPN
          YT.A..TV.YS.NKIDD.IRYLSL..NKYIRYF.GH.K.VV.LSMSP.D.TFISGS.DKTIRLWDLRSPN
Retrocopy YTRAESTVIYSCNKIDDAIRYLSLPENKYIRYFHGHKKTVVTLSMSPSDETFISGSIDKTIRLWDLRSPN

Parental  CQGLMHLQGKPVCSFDPEGLIFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDRNCEWTGLKFSNDGKLIL
          CQGLMHLQGKPVCSFDPEGLIFAAGVNSEM.KLYDLRSFDKGPFATF.M..D...EWTGLKFS.DGK.IL
Retrocopy CQGLMHLQGKPVCSFDPEGLIFAAGVNSEMIKLYDLRSFDKGPFATFRMEQDKTYEWTGLKFSKDGKHIL

Parental  ISTNGSFIRLIDAFKGAVMHTFGGYNNSKAVTLEASFTPDSQFIMIGSDDGKIHVWNGESGIKVAVLDGK
          ..TNGS.....DAFKG.V.H.F.GYNN..A..LEA.FTPDSQF.MIGS.DGKIH.WNGE.G.KVAVLD.K
Retrocopy LYTNGSCFHVVDAFKGIVTHIFSGYNNHQALSLEAAFTPDSQFVMIGSEDGKIHIWNGENGEKVAVLDAK

Parental  HTGPITCLQFNPKFMTFASACSNMAFWLPTIDD
          HTGPITCLQFNP.FMTFASACSNM.FWLPTIDD
Retrocopy HTGPITCLQFNPNFMTFASACSNMSFWLPTIDD

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_219 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_219 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000774	1 retrocopy	retro_chof_2299,
Callithrix jacchus	ENSCJAG00000006114	1 retrocopy	retro_cjac_3022,
Homo sapiens	ENSG00000164091	2 retrocopies	retro_hsap_2816, retro_hsap_419,
Loxodonta africana	ENSLAFG00000028309	1 retrocopy	retro_lafr_639,
Macropus eugenii	ENSMEUG00000009280	1 retrocopy	retro_meug_1207,
Macaca mulatta	ENSMMUG00000008234	2 retrocopies	retro_mmul_339, retro_mmul_511,
Monodelphis domestica	ENSMODG00000011614	4 retrocopies	retro_mdom_1259, retro_mdom_144, retro_mdom_219 , retro_mdom_398,
Nomascus leucogenys	ENSNLEG00000007104	2 retrocopies	retro_nleu_1016, retro_nleu_1195,
Otolemur garnettii	ENSOGAG00000016032	1 retrocopy	retro_ogar_1314,
Pongo abelii	ENSPPYG00000013812	2 retrocopies	retro_pabe_185, retro_pabe_300,
Rattus norvegicus	ENSRNOG00000048441	3 retrocopies	retro_rnor_1003, retro_rnor_1109, retro_rnor_1152,