RetrogeneDB ID: retro_mdom_433

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:514488593..514489095(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAX1
• Ensembl ID: ENSMODG00000017215
• Aliases: None
• Description: HCLS1 associated protein X-1 [Source:HGNC Symbol;Acc:16915]

Sequence

>retro_mdom_433
GGCTTAGAGCCAGAAGCCCCAAATGAGACACTGAGGGAAGGGGAGATTATCTGGGATTTGATGCTCGGCATCCAGATAGT
CACCAGCCTAGGATTTTTAGTGGGAGTTCAGAGAGTGATCTGGGGCACTTATTTGCCAAAGTAGTCTCAGACTAGGACCC
TAAGAGGCCTTTTCATGGATTTGGTGACAGGTGGCCAGTGATCTCTGATGCTAGAACCAGAGAGGACAAGAATTTGATTT
CCAGATCTCACAGGAGGACCTGGGTCAAGTCCTCCAGCCCCAGCCCAAGTGATATTTCAGAAGCATCTCAGTTACCAAGA
AAACTGGGCCAGATCTGATGGTGGAGGAGCATTTCACTGTTATCAACTGTGAGGGTCACAAAGAAACCACATGAACTCCT
TGAGAAGCAGATGGAAGTTCTGGAGATGATTCAGGCATCCCATGGCCTCCAGACTTAGGGGACAGTTCTTCCATCCTGGA
TTTATTCCTAGGACAATGGTTC

Alignment

ORF - retro_mdom_433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.18 %
• Parental protein coverage: 61.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPEPEAPNERQREGETIRDSML-KYPDSHQPKIFSGSSESEAGHSSPKVGPDWDSKRPLRSFGDRWPVIS
          G.EPEAPNE..REGE.I.D.ML...PDSHQP.IFSGSSES..GH...KV..D.D.KRP...FGDRWPVIS
Retrocopy GLEPEAPNETLREGEIIWDLML<RHPDSHQPRIFSGSSESDLGHLFAKVVSD*DPKRPFHGFGDRWPVIS

Parental  DARTKEDKDL-DSQVSKEGLGQVLQPQPKSYFRSVSVTKITGPDGTVEERRTVVDSEGHKETTVTRREAD
          DART.EDK.L.D.Q.S.E.LGQVLQPQPK.YFRS.SVTK.TGPD..VEE..TV...EGHKETT.T..EAD
Retrocopy DARTREDKNL<DFQISQEDLGQVLQPQPK*YFRSISVTKKTGPDLMVEEHFTVINCEGHKETT*TP*EAD

Parental  GSYRDDSGTPQPPDLGDSSSILNSFLGRWF
          GS..DDSG.P.PPDLGDSSSIL..FLG.WF
Retrocopy GSSGDDSGIPWPPDLGDSSSILDLFLGQWF

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	0.24 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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_433 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_433 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433 ,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,