RetrogeneDB ID: retro_mdom_700

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:157266451..157266966(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CA10
• Ensembl ID: ENSMODG00000012548
• Aliases: None
• Description: carbonic anhydrase X [Source:HGNC Symbol;Acc:1369]

Sequence

>retro_mdom_700
GTTCAGCTAATCCACTATAACCATGAGTTATATACAAATGTCACAGAGGCTGCAAAAAGTCCAAATGGATTGGTAGTAGT
TTCTACATTTATGAAAGTTTCTGATCAAATCCATTTCTTAATCGAATGCTCAACAGAGATACCATCACAAGAATAACGTA
TAAAAATGATGCATGCTTGCTTCAGGGACTTAATATAGAGGAACTATATCCTGAGACCTCTAGCTTCATTACCTACGATG
GGTCAATGACTATCCCACCCTGTTATGAGGCAGCAAGTTGGATAATAATGAACAAACCAGTCTACATAACCAGGATGCAG
ATGTATTCCTTATGACTGCTCAGCCAGAATCAGCCATCTCAGATCTTTCTGAGCATGAGTGACAACTTCCAGCCTGTTCA
GCCACTCAATAACCGTTGCATCCGTACCAACATCAACTTTAGTTTACAAGGGAAAGACTGTCCAAATAACAGAGCCCAGA
AGCTACAATATAGAGTAAACGAATGGCTGCTCAAG

Alignment

ORF - retro_mdom_700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 56.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VQLIHYNHELYTNVTEAAKSPNGLVVV-SIFMKVSDSSNPFLNRMLNRDTITRITYKNDAYLLQGLNIEE
          VQLIHYNHELYTNVTEAAKSPNGL.VV.S.....S..SNPFLNRMLNRDTITRITYKNDA.LLQGLNIEE
Retrocopy VQLIHYNHELYTNVTEAAKSPNGL-VV<SFYIYESF*SNPFLNRMLNRDTITRITYKNDACLLQGLNIEE

Parental  LYPETSSFITYDGSMTIPPCYETASWIIMNKPVYITRMQMHSLRLLSQNQPSQIFLSMSDNFRPVQPLNN
          LYPETSSFITYDGSMTIPPCYE.ASWIIMNKPVYITRMQM.SL.LLSQNQPSQIFLSMSDNF.PVQPLNN
Retrocopy LYPETSSFITYDGSMTIPPCYEAASWIIMNKPVYITRMQMYSL*LLSQNQPSQIFLSMSDNFQPVQPLNN

Parental  RCIRTNINFSLQGKDCPNNRAQKLQYRVNEWLLK
          RCIRTNINFSLQGKDCPNNRAQKLQYRVNEWLLK
Retrocopy RCIRTNINFSLQGKDCPNNRAQKLQYRVNEWLLK

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_700 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_700 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009007	1 retrocopy	retro_chof_855,
Dasypus novemcinctus	ENSDNOG00000010755	1 retrocopy	retro_dnov_512,
Monodelphis domestica	ENSMODG00000012548	1 retrocopy	retro_mdom_700 ,