RetrogeneDB ID: retro_mdom_574

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:356012720..356013196(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005014
• Aliases: None
• Description: None

Sequence

>retro_mdom_574
ATGACCACTCCAGGACCACATAATGCTGTTCCATTAGGAGCATCTGCTCCAACAGTATCTCCTCCTAAGAAGAGACGATG
GCGATCAATAGTTATTATCCTACTCCCCCCCCCCCCCAACCCGTGCCAGGAGTGGTACCTGGGGCGGATGGGAAGGGCAT
GAATCCTTCTGCGTACTATTCTCAGCCTCTACCAGTTCCTAATCCTAATGCAGTTGCGCTTCAGACTGCGTACATGCAGC
AGCCTGTCTCCTTTTTTGACCACCCGGTCCAGATGTGCTGTCCTTCGTGTAACAAGATGATAGTGACCAGACTCTCCTAT
AACGCAGACGCCCTAACCTGGCTTTCGTGCGGCAGCCTTTGCTTATTGGGATGTATAGCCTGCTGCTGCTTCATTCCCTT
CTGTGCCGACGCCGTTCAGGATGTCGATCACTATTGCCCAAATTGCAAAGCTCTTCTTGGTACCTATAAACGTTTG

Alignment

ORF - retro_mdom_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTPGPHNAVPGGASAPTAPPTY-EETMAINSYYPTPPPG-PVPGVVPGADGKGMNPPAYYTQPLPVPNP
          MTTPGPHNAVP.GASAPT..P...EETMAINSYYPT.....PVPGVVPGADGKGMNP.AYY.QPLPVPNP
Retrocopy MTTPGPHNAVPLGASAPTVSPPK<EETMAINSYYPTXXXXXPVPGVVPGADGKGMNPSAYYSQPLPVPNP

Parental  NAIAVQTVYVQQPVSFFDRPVQMCCPSCNKMIVTSLSYNAGALTWLSCGSLCLLGCIAGCCFIPFCVDAL
          NA.A.QT.Y.QQPVSFFD.PVQMCCPSCNKMIVT.LSYNA.ALTWLSCGSLCLLGCIA.CCFIPFC.DA.
Retrocopy NAVALQTAYMQQPVSFFDHPVQMCCPSCNKMIVTRLSYNADALTWLSCGSLCLLGCIACCCFIPFCADAV

Parental  QDVDHYCPNCKALLGTYKRL
          QDVDHYCPNCKALLGTYKRL
Retrocopy QDVDHYCPNCKALLGTYKRL

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_574 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_574 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006659	1 retrocopy	retro_cpor_704,
Macaca mulatta	ENSMMUG00000008784	1 retrocopy	retro_mmul_1411,
Monodelphis domestica	ENSMODG00000005014	4 retrocopies	retro_mdom_174, retro_mdom_574 , retro_mdom_887, retro_mdom_911,
Otolemur garnettii	ENSOGAG00000028239	2 retrocopies	retro_ogar_1479, retro_ogar_2820,
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261,
Rattus norvegicus	ENSRNOG00000002520	1 retrocopy	retro_rnor_2056,
Tupaia belangeri	ENSTBEG00000017097	1 retrocopy	retro_tbel_4388,
Tursiops truncatus	ENSTTRG00000010854	1 retrocopy	retro_ttru_1244,