RetrogeneDB ID: retro_mdom_1340

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:67186778..67187236(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPP21
• Ensembl ID: ENSMODG00000015967
• Aliases: None
• Description: ribonuclease P/MRP 21kDa subunit [Source:HGNC Symbol;Acc:21300]

Sequence

>retro_mdom_1340
ATGGTGGGCCAGGTGAAGGACAAGGAGGCTTTTCAGAGACTCAGCTTCTTGTACTCGGCTGCCCATCGCGTCCTAGCCCA
GAACCCCAAGAACCAGGTGCTGGCGATGTTTTACTGCCACATGGAGAGAACCATTAGGAAGAGGCTCATCCTGCGACAGG
ACCCCTCAGTGAAAAGGACCCTCTGTTGTGGCTGCTCCTCCCTCCTCATTCCCATTTGACTTGCACCCAGTGGCAGAGGC
ATTGCCTAGGGCAGTGCTGGACAGTACAGACCTGTCTAACATGCCATTGAAGCTGAAGATTCCTCAATGACCCCAAACAC
CAGCTCTGGGGGTACTGGCCTGAGGTGCAGCAGGGGAATCAGGCTGATCTCAAATCAAATAAGCCTGTGGCACCCACGAG
CCATCCAGCCTCAGTCCAGCCTTCTGGAGGGAAATCCAAGCATCAGATCCTCAAAATA

Alignment

ORF - retro_mdom_1340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGQVKDKEAFQRLSFLYQAAHCVLAQNPENQALARFYCHTERTIGKRLVLRQDPSVKRTLCRGCSSLLV
          M.GQVKDKEAFQRLSFLY.AAH.VLAQNP.NQ.LA.FYCH.ERTI.KRL.LRQDPSVKRTLC.GCSSLL.
Retrocopy MVGQVKDKEAFQRLSFLYSAAHRVLAQNPKNQVLAMFYCHMERTIRKRLILRQDPSVKRTLCCGCSSLLI

Parental  P-GLTCTQRQRRHLGQRWTVQTCLTCHRSRRYLNDPKHQLWGDRPEAQQGNQADLKSNKPVAPTNHPVSV
          P..LTCTQ.QR..LGQ.WTVQTCLTCH.S.R.LNDPKHQLWG..PE.QQGNQADLKSNKPVAPT.HP.SV
Retrocopy P<HLTCTQWQRHCLGQCWTVQTCLTCH*S*RFLNDPKHQLWGYWPEVQQGNQADLKSNKPVAPTSHPASV

Parental  QPSGGKSEPQIPKI
          QPSGGKS..QI.KI
Retrocopy QPSGGKSKHQILKI

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_1340 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1340 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012222	1 retrocopy	retro_chof_69,
Loxodonta africana	ENSLAFG00000010777	1 retrocopy	retro_lafr_630,
Monodelphis domestica	ENSMODG00000015967	2 retrocopies	retro_mdom_1142, retro_mdom_1340 ,