RetrogeneDB ID: retro_mdom_568

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:328020550..328021144(-)
• Located in intron of: ENSMODG00000012586

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM81A
• Ensembl ID: ENSMODG00000008897
• Aliases: None
• Description: family with sequence similarity 81, member A [Source:HGNC Symbol;Acc:28379]

Sequence

>retro_mdom_568
ATTTTGGAAACTAAAATCAAAGATGCAGAAGGACAGATTTCTCAATTTTTAAGCAGAGTTGACCTGCCATTATCAGAGCA
AAGCACAAAGCTGAAAATGACCCACAGAGATAGCAACCATCAGCTTCACCCTTTGGACATTAAATTTAAAGGTACAGTAG
AAGAACTTAGTAGCCAAATTTTGTCTGCACGGAATTGGTTGCAACAGGAACAAAAACAGATAGAAAAAGAACTTTTATAG
AAGATTGATCAACTTGCATTGATTGTTAAGGAAAATAGTGAAATTAGTGAAAGGACAATAGAGAAGTTCAGTCAGATGTC
AGCAAAGCTTGATAAAATAGAAGAGATACAAAAGAAAAATGTGGACGCACAGAGGCCAAAATCTGATGATGAGAAGATGA
ATGTCCGAATCAGCAAAATTGAGTTGCAGATGAATGAAGAGATGAAAGAAATGAAAGCAGAAGTTAATGCTGGATTTACA
GCCATCTATGAAAGCATAGGATCACTCAGACAAGTTCTTGAAGTCAAAATGAAAATTGATAAAGGCCAGCTACTGAAACA
AATTCATCAGCTAAGGAAGCAAGAGACTCCCATG

Alignment

ORF - retro_mdom_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.47 %
• Parental protein coverage: 52.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILETKIKDAEGQISQLLSRVDLSLSEQSTKLKMTHRDSNHQLHLLDIKFKGTVEELSSQILSARNWLQQE
          ILETKIKDAEGQISQ.LSRVDL.LSEQSTKLKMTHRDSNHQLH.LDIKFKGTVEELSSQILSARNWLQQE
Retrocopy ILETKIKDAEGQISQFLSRVDLPLSEQSTKLKMTHRDSNHQLHPLDIKFKGTVEELSSQILSARNWLQQE

Parental  QERIEKELLQKIDQLALVVKENSEISERTIEKKFSQMSAKLDKIEEIQKKNMDAQRPKSDDEKMNVRISK
          Q..IEKELL.KIDQLAL.VKENSEISERTIE.KFSQMSAKLDKIEEIQKKN.DAQRPKSDDEKMNVRISK
Retrocopy QKQIEKELL*KIDQLALIVKENSEISERTIE-KFSQMSAKLDKIEEIQKKNVDAQRPKSDDEKMNVRISK

Parental  IELQMNEEMKEMKAEVNAGFAAIYESIGSLRQVLEAKMKIDKDQLLKQIHQLRKQEAPM
          IELQMNEEMKEMKAEVNAGF.AIYESIGSLRQVLE.KMKIDK.QLLKQIHQLRKQE.PM
Retrocopy IELQMNEEMKEMKAEVNAGFTAIYESIGSLRQVLEVKMKIDKGQLLKQIHQLRKQETPM

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	95.24 RPM
SRP007412_cerebellum	0.00 RPM	0.98 RPM
SRP007412_heart	0.00 RPM	3.19 RPM
SRP007412_kidney	0.00 RPM	27.65 RPM
SRP007412_liver	0.00 RPM	0.50 RPM
SRP007412_testis	0.00 RPM	2.95 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_568 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_568 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000008897	2 retrocopies	retro_mdom_1537, retro_mdom_568 ,