RetrogeneDB ID: retro_mdom_1275

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:214089249..214089555(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA0101
• Ensembl ID: ENSMODG00000027710
• Aliases: None
• Description: KIAA0101 [Source:HGNC Symbol;Acc:28961]

Sequence

>retro_mdom_1275
GTGGTGGCAGCTCAGGTACCCCAGAAGGTTCTCGGTCATTCCAGCTTCTCCAGTTCCTCTCTCTCGCCTCCATCCAGGAA
AGCCGAAAATAAGTATGCAGGTGGAAACCCAGTATTTGTATGACCAACACGTACATGGCAAAAAGGAATTGGAGAATTCT
TTGGGATGTCATCTAAACCTTCAGAAAAATAGAATCAGATTCCTGATGAAGCAGAAGCAGGAAGTAGTGGCCTAGGACAA
CCTAAAAGAAAATCTTGTCCTTTGCGACCTGATCCCACAGAGGATGATGAATGTCCAGATGAAGAA

Alignment

ORF - retro_mdom_1275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.27 %
• Parental protein coverage: 87.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVAARAPRKVLGHSSFANSSPSPLSRKAESKYAGGNPVCVRPTPTWQKGIGEFFGMSSKPSEKENQIPDE
          VVAA..P.KVLGHSSF..SS.SP.SRKAE.KYAGGNPV.V.PT.TWQKGIGEFFGMSSKPSEK.NQIPDE
Retrocopy VVAAQVPQKVLGHSSFSSSSLSPPSRKAENKYAGGNPVFV*PTRTWQKGIGEFFGMSSKPSEK*NQIPDE

Parental  AEAGSSGLGKPKRKSYPLRPDPTEDDECPDEE
          AEAGSSGLG.PKRKS.PLRPDPTEDDECPDEE
Retrocopy AEAGSSGLGQPKRKSCPLRPDPTEDDECPDEE

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	1.31 RPM
SRP007412_cerebellum	0.00 RPM	0.98 RPM
SRP007412_heart	0.00 RPM	0.20 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	1.51 RPM
SRP007412_testis	0.00 RPM	8.84 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1275 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1275 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 9 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010763	2 retrocopies	retro_chof_1104, retro_chof_892,
Cavia porcellus	ENSCPOG00000006482	3 retrocopies	retro_cpor_138, retro_cpor_186, retro_cpor_365,
Dipodomys ordii	ENSDORG00000014912	1 retrocopy	retro_dord_674,
Monodelphis domestica	ENSMODG00000027710	2 retrocopies	retro_mdom_1275 , retro_mdom_776,
Mus musculus	ENSMUSG00000040204	7 retrocopies	retro_mmus_1088, retro_mmus_1289, retro_mmus_1335, retro_mmus_1844, retro_mmus_2809, retro_mmus_2964, retro_mmus_378,
Otolemur garnettii	ENSOGAG00000003982	1 retrocopy	retro_ogar_501,
Rattus norvegicus	ENSRNOG00000016561	5 retrocopies	retro_rnor_1162, retro_rnor_1412, retro_rnor_2595, retro_rnor_2624, retro_rnor_2698,
Ictidomys tridecemlineatus	ENSSTOG00000019643	4 retrocopies	retro_itri_1241, retro_itri_1324, retro_itri_1888, retro_itri_929,
Tupaia belangeri	ENSTBEG00000013732	2 retrocopies	retro_tbel_3099, retro_tbel_4093,