RetrogeneDB ID: retro_mdom_860

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:229313836..229314334(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002661
• Aliases: None
• Description: None

Sequence

>retro_mdom_860
CAGGGCAACAAAGGCAACAGCAACAGGAGCTTGGGAGGCCTGCCAGGTTCTTTGGTGGGAGTGGCGGCGGGCCTAGCTAC
TCGAACACAGATTTGGCTGGAGTTCCTCTTACTGGTATGAGTCCTCTGTCTCCATATTTAAATGTGGATCCCAGATATCT
TATACAGGACACAGATGAGTTTATTTTACCCACTGGAGCCAATAAAACCCGGGGCAGGTTTGAATTGGCCTTTTTTTTTT
TTACCATTGGAGGATGCTGTATAACAGGAGCTGCATTTGGAGCCATGAATGGTTTAAGACTGGGATTGAAGGAGACACAA
AAAAATGTCCTGGTCCAAGCCAAGAAATGTACAGATTTTGAATATGGTAACCAGGCAAGGAGCACTATGGACTAATACTC
TGGGCTCTCTGGCTCTGCTCTGCAGTGCATTTCATGTTGTCATAGAAAAAACTCGAGGTGCAGAAGATGACATCAATACA
GTAGCAGCTGGGACCATA

Alignment

ORF - retro_mdom_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.07 %
• Parental protein coverage: 77.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGNGGNSNRSSGGLAG-FFGGSGGGPSYSNADLAGVPLTGMSPLSPYLNVDPRYLIQDTDEFILPTGANK
          .GN.GNSNRS.GGL.G.FFGGSGGGPSYSN.DLAGVPLTGMSPLSPYLNVDPRYLIQDTDEFILPTGANK
Retrocopy QGNKGNSNRSLGGLPG<FFGGSGGGPSYSNTDLAGVPLTGMSPLSPYLNVDPRYLIQDTDEFILPTGANK

Parental  TRGRFELA--FFTIGGCCITGAAFGAMNGLRLGLKETQ-KMSWSKPRNVQILNMVTRQGALWANTLGSLA
          TRGRFELA....TIGGCCITGAAFGAMNGLRLGLKETQ.KMSWSKPRNVQILNMVTRQGALW.NTLGSLA
Retrocopy TRGRFELAXXXXTIGGCCITGAAFGAMNGLRLGLKETQ>KMSWSKPRNVQILNMVTRQGALWTNTLGSLA

Parental  LLYSAFGVVIEKTRGAEDDINTVAAGTM
          LL.SAF.VVIEKTRGAEDDINTVAAGT.
Retrocopy LLCSAFHVVIEKTRGAEDDINTVAAGTI

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	215.15 RPM
SRP007412_cerebellum	0.00 RPM	243.21 RPM
SRP007412_heart	0.00 RPM	328.13 RPM
SRP007412_kidney	0.00 RPM	341.06 RPM
SRP007412_liver	0.00 RPM	328.78 RPM
SRP007412_testis	0.00 RPM	478.12 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_860 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_860 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 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007501	1 retrocopy	retro_amel_1488,
Canis familiaris	ENSCAFG00000029477	1 retrocopy	retro_cfam_329,
Choloepus hoffmanni	ENSCHOG00000007073	1 retrocopy	retro_chof_797,
Callithrix jacchus	ENSCJAG00000013336	1 retrocopy	retro_cjac_2965,
Cavia porcellus	ENSCPOG00000019917	2 retrocopies	retro_cpor_1013, retro_cpor_321,
Monodelphis domestica	ENSMODG00000002661	2 retrocopies	retro_mdom_1202, retro_mdom_860 ,
Mus musculus	ENSMUSG00000013701	1 retrocopy	retro_mmus_2,
Oryctolagus cuniculus	ENSOCUG00000000525	1 retrocopy	retro_ocun_73,
Otolemur garnettii	ENSOGAG00000015393	1 retrocopy	retro_ogar_2627,
Ochotona princeps	ENSOPRG00000005255	2 retrocopies	retro_opri_520, retro_opri_920,
Procavia capensis	ENSPCAG00000015914	1 retrocopy	retro_pcap_181,
Rattus norvegicus	ENSRNOG00000019811	3 retrocopies	retro_rnor_1804, retro_rnor_225, retro_rnor_661,
Sorex araneus	ENSSARG00000010335	1 retrocopy	retro_sara_86,
Sus scrofa	ENSSSCG00000025276	1 retrocopy	retro_sscr_404,
Ictidomys tridecemlineatus	ENSSTOG00000007041	1 retrocopy	retro_itri_1043,