RetrogeneDB ID: retro_mdom_1922

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:150334651..150335695(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000017117
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAB21L3
• Ensembl ID: ENSMODG00000004947
• Aliases: None
• Description: mab-21-like 3 (C. elegans) [Source:HGNC Symbol;Acc:26787]

Sequence

>retro_mdom_1922
AAGGTGGAGCTGAGACAAAATACCATCTCCAAGACTGTAGAAGAGGTGAAGAAAATCATCCATGAATTGACCTCAGTAAT
CAGTCTCAAAAGACATTAGATTCCAACCCATTTCTAAATCAGACCTTAACAATGAGAACATAAAGGTTTTGGCACCTAAC
CAATTCTTTATCACAGTCCCCCTTAAAGCATTGGTTAGGTATAAAAAACAACAGAACCGAAGGTGGCGGTATTATTCCTT
GAGTGGCTCTCCCCAGGTCTCTCCAGTTCCGGATCCTGAAGATTTGTACCAATGGCTGGAAGTAAATCAGTTTTTGAAGT
CTCTGCAGCAGTGGCATGAAATGGATGTGATTATGGAAGGAGACATCATACCAGCAAAGGTCCTTCAAGTGTTCCGGAAT
CTAGTGGATATCTCAATTAAGACCTGCAGCTGCTCTAGAAAAGCCAACCTACTAGACTCTTATGGTTCCACAGTTCGACT
AGAAATAGAGACATCAGTATGTCAGGTGGAAGTAGAATTGGTTCCTGTGGTAGAGATCTTCAACCAATGGTGTGACAAGG
CTTGGTGGCCTCGGTGTTCGAAGCGGTGGCCTTCTCAGGAGAAAGCAGAATGTGTTAAGTCAATTGGGTTTAGCCTGATG
GCTTGCTCCAGTTTCCACTGGCAATTGAACTTCTCTCAAGCTGAGTATATGCTGATGGAGGGGATAGATAAGGACGGTGG
TTGCCGAAAGACATGTTTCCAGGTCCTGAGGCAGATGAAAGAGTATGTTTGGTGTCCCGGAAACAGACCTATCATCACAT
CTCAGCATCTTAAGATGGTTCTGTTTTGGACTTGTGAGAAGTACCCACATGCCAAAGACTGGAAAATTTTCACAGTATCC
TTTCTGCGCCTGGTCCATAAGCTGCACAAGTGTGTGTCCCAGCACTTCTTGAAACATATTTTGTTGATAGAAACAACATG
TTTCAGTATGTCAGCATAAATGACTTGGATGCCATAGCCCAAAAGCTGACCCTTTTTCTAGAGAATCCAGTACTCTGCTG
GACC

Alignment

ORF - retro_mdom_1922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.57 %
• Parental protein coverage: 97.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVELRQSTISKTVEEVKKIIHELTSVISLK-DIRFQPISKSDLYNENIKVLAPNQFLITVPLKGLVGYKK
          .VELRQ.TISKTVEEVKKIIHELTSVISLK.DIRFQPISKSDL.NENIKVLAPNQF.ITVPLK.LV.YKK
Retrocopy KVELRQNTISKTVEEVKKIIHELTSVISLK>DIRFQPISKSDLNNENIKVLAPNQFFITVPLKALVRYKK

Parental  QQNRRWRYYSLSGSPQVSPVRDPEDLYQWLEVNQFLKSLQQWHEMDVIMEGDIIPAKVLQVFRNLVDISI
          QQNRRWRYYSLSGSPQVSPV.DPEDLYQWLEVNQFLKSLQQWHEMDVIMEGDIIPAKVLQVFRNLVDISI
Retrocopy QQNRRWRYYSLSGSPQVSPVPDPEDLYQWLEVNQFLKSLQQWHEMDVIMEGDIIPAKVLQVFRNLVDISI

Parental  KTCSCSRKANLLESYGSTVRLEIETSVCQVEVELVPVVEIFNQWCDKARWPRCLKRWPSREKAECVKSIG
          KTCSCSRKANLL.SYGSTVRLEIETSVCQVEVELVPVVEIFNQWCDKA.WPRC.KRWPS.EKAECVKSIG
Retrocopy KTCSCSRKANLLDSYGSTVRLEIETSVCQVEVELVPVVEIFNQWCDKAWWPRCSKRWPSQEKAECVKSIG

Parental  FSLMACSRFHWQLNFSQAEYMLMEGIDEDGGCRKICFQVLRQMKEDVWCPGNRPIITSQHLKMVLFWTCE
          FSLMACS.FHWQLNFSQAEYMLMEGID.DGGCRK.CFQVLRQMKE.VWCPGNRPIITSQHLKMVLFWTCE
Retrocopy FSLMACSSFHWQLNFSQAEYMLMEGIDKDGGCRKTCFQVLRQMKEYVWCPGNRPIITSQHLKMVLFWTCE

Parental  KYPHAKDWKIFTVSFLRLVRKLHKCVSQHFLKH-YFVDGNNMFQYVSINDLDAIAQKLTLFLENPVLCWT
          KYPHAKDWKIFTVSFLRLV.KLHKCVSQHFLKH.YFVD.NNMFQYVSINDLDAIAQKLTLFLENPVLCWT
Retrocopy KYPHAKDWKIFTVSFLRLVHKLHKCVSQHFLKH<YFVDRNNMFQYVSINDLDAIAQKLTLFLENPVLCWT

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_1922 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1922 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	ENSMODG00000004947	2 retrocopies	retro_mdom_1922 , retro_mdom_676,