RetrogeneDB ID: retro_mdom_245

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:164015105..164016077(+)
• Located in intron of: ENSMODG00000015420

Retrocopy information

• Ensembl ID: ENSMODG00000015425
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000015986
• Aliases: None
• Description: None

Sequence

>retro_mdom_245
ATGGAAGGACCAAATCCCTTCAAGACACCTAGCAAATTACCTGAGAAGAAGAAATCTTCATCATGCTTAACTCCATCATC
TGTAGCTATTCCAGCTTCTCCATTTATGAAAAAGCTTGGCTATGGCACTGGAGTAAATGTTTACCTTATGAAAAAGTCTC
CCAAAGGCTTGTCTCGTTCTCCTTGGGCAGTGAAAAAGATTAATTCCAAATGTAATGATCATTATCAAAGTATATATCAA
AAGAGACTAAATGATGAAGCTAAGATTTTGAAAGACCTTCAGCATCCAAACATTGTAGGTTATCAGGCATTTGCTCCAGC
CCAGGATGGAAGTATGTGTCGTGCTATGGAGTATGGAGGAGAAAAGTCTCTCAATGACTTAATTGAGGAAAGAAATACCA
ACTGCCATTCTCCTTTCCCAGCTGCTATAATTTTGAAGGTTGCTTTGCACATGGCAAGGGGGTTAAAGTATCTGCACCAA
GAAAAGAAGCTCCTACATGGAGATATAAAGTCTTCAAATGTCGTAATTAAAGGTGATTTTGAAGCAATTAAAATCTGTGA
CGTAGGAGTCTCACTGCCACTGGATGAAAATATGACTGTGAGTGACCCTGAGGCGCATTACATTAGCACAGAACCCTGGA
AACCAAAGGAAGCTCTGGAAGAATGTGGTATCATTACTGATAAAGCTGACATATTTGCCTTTGGCCTAACTCTTTGGGAG
ATGTTGACCCTAACCATTCCACATGTTAATCTTCCAGAGGATGAGGATGATGAAGACAAAATTTTTGATGAGAGCATGTT
TGATGATGAAGCATACTATGAAGCACTGGGAACAAGGCCAGCCATTAATATGGAAGAATTGGATGAATCATATCAAAAAG
TAATTGAACTGTTTTCTATTTGCACTAATGAGAATCCTAAAGACCGTCCCTCAGCTGCATACATAGTTGAAGCTTTGGAA
ATAAATATGTAA

Alignment

ORF - retro_mdom_245 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.41 %
• Parental protein coverage: 70.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YRAFAQAQDGSMCLAMEYGGEKSLNDLIEERNTNCHSPFPAAIILKVALHMARGLKYLHQEKKLLHGDIK
          Y.AFA.AQDGSMC.AMEYGGEKSLNDLIEERNTNCHSPFPAAIILKVALHMARGLKYLHQEKKLLHGDIK
Retrocopy YQAFAPAQDGSMCRAMEYGGEKSLNDLIEERNTNCHSPFPAAIILKVALHMARGLKYLHQEKKLLHGDIK

Parental  SSNVVIKGDFEAIKICDVGVSLPLDENMTVSDPEAHYIGTEPWKPKEALEECGIITDKADIFAFGLTLWE
          SSNVVIKGDFEAIKICDVGVSLPLDENMTVSDPEAHYI.TEPWKPKEALEECGIITDKADIFAFGLTLWE
Retrocopy SSNVVIKGDFEAIKICDVGVSLPLDENMTVSDPEAHYISTEPWKPKEALEECGIITDKADIFAFGLTLWE

Parental  MLTLTIPHVNLPEDEDDEDKTFDESMFDDEAYYEALGTRPAINMEELDESYQKVIELFSVCTNENPKDRP
          MLTLTIPHVNLPEDEDDEDK.FDESMFDDEAYYEALGTRPAINMEELDESYQKVIELFS.CTNENPKDRP
Retrocopy MLTLTIPHVNLPEDEDDEDKIFDESMFDDEAYYEALGTRPAINMEELDESYQKVIELFSICTNENPKDRP

Parental  SAAYIVEALEMNI
          SAAYIVEALE.N.
Retrocopy SAAYIVEALEINM

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	0.12 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.20 RPM
SRP007412_kidney	0.00 RPM	1.32 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	9.43 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_245 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_245 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021069	1 retrocopy	retro_btau_150,
Canis familiaris	ENSCAFG00000008369	1 retrocopy	retro_cfam_1694,
Dipodomys ordii	ENSDORG00000014896	1 retrocopy	retro_dord_697,
Myotis lucifugus	ENSMLUG00000009596	1 retrocopy	retro_mluc_713,
Monodelphis domestica	ENSMODG00000015986	1 retrocopy	retro_mdom_245 ,
Mus musculus	ENSMUSG00000022033	1 retrocopy	retro_mmus_2452,
Otolemur garnettii	ENSOGAG00000009887	1 retrocopy	retro_ogar_3495,
Tupaia belangeri	ENSTBEG00000002239	1 retrocopy	retro_tbel_3290,