RetrogeneDB ID: retro_mdom_1828

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:29204428..29204847(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPC25
• Ensembl ID: ENSMODG00000007753
• Aliases: None
• Description: SPC25, NDC80 kinetochore complex component [Source:HGNC Symbol;Acc:24031]

Sequence

>retro_mdom_1828
GTGATGTCACACATAAAGACAGAAGAGAAATTGGACTTATTTAATAAAAGTGTAAATGACTTTTAGACCAAATTACAAAA
TACTACACTCAATGAATACTGTTTTCAAATGGTGGGATTGAGAGATAACTATGAAAGCTCCATTGAAGCACTGACAGAAA
AATTGCCCACAAAGATAAAAGAAGATGATTGGATGATTGAGACTTTTTTGGAATTCAGAAATAAGATTTGCATCCAGAAT
AAGCTTATTCAGGAAAAACAACATCGTTGATTAAATGTGGCTGACAGTACACAAAACAGGAATGCGAAATGGAAAAGGCA
GCCACAAATGCGTAAGATCTACTGAAAAAGAAAGAAGAAATTATTTACACCAACAACAAAGCCAACAAGGAAAGGTTGAA
AATACCACAGAAATCTTTT

Alignment

ORF - retro_mdom_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.36 %
• Parental protein coverage: 60.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMSHIKTEEELDLFNKSINDFWNKFRNTTLNEHCSQMVGLRDTYKDSIEALTERLSTKIKEEDRMIETFL
          .MSHIKTEE.LDLFNKS.NDF..K..NTTLNE.C.QMVGLRD.Y..SIEALTE.L.TKIKE.D.MIETFL
Retrocopy VMSHIKTEEKLDLFNKSVNDF*TKLQNTTLNEYCFQMVGLRDNYESSIEALTEKLPTKIKEDDWMIETFL

Parental  EFRNTIHIQNKLIQEKQDNLLKLVDGIQDK-EREMEKLTERIQDLKESLDKKKEIISAANKANKERLKML
          EFRN.I.IQNKLIQEKQ...L...D..Q...E.EMEK......DL...L.KK.EII...NKANKERLK..
Retrocopy EFRNKICIQNKLIQEKQHR*LNVADSTQNR<ECEMEKAATNA*DL---LKKKEEIIYTNNKANKERLKIP

Parental  QKSY
          QKS.
Retrocopy QKSF

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_1828 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1828 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013303	4 retrocopies	retro_chof_1070, retro_chof_1541, retro_chof_2326, retro_chof_744,
Cavia porcellus	ENSCPOG00000005926	1 retrocopy	retro_cpor_1032,
Dasypus novemcinctus	ENSDNOG00000004429	1 retrocopy	retro_dnov_826,
Echinops telfairi	ENSETEG00000015642	1 retrocopy	retro_etel_1554,
Loxodonta africana	ENSLAFG00000004668	1 retrocopy	retro_lafr_497,
Monodelphis domestica	ENSMODG00000007753	1 retrocopy	retro_mdom_1828 ,
Tupaia belangeri	ENSTBEG00000012559	1 retrocopy	retro_tbel_2798,
Tursiops truncatus	ENSTTRG00000006112	1 retrocopy	retro_ttru_574,