RetrogeneDB ID: retro_mdom_320

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:120148749..120149242(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPIA
• Ensembl ID: ENSMODG00000009649
• Aliases: None
• Description: ribose 5-phosphate isomerase A [Source:HGNC Symbol;Acc:10297]

Sequence

>retro_mdom_320
CCTGCAGAATGGCTTACCCAACACCCCGGGCTGGATCTTGCTATTGATGATGCGGATGAAGTTGTCACCAACCTCAATCT
TATCAAAGGTGGCGGAGGCTGTCTGACCCAGGAGAAAATGGTAGCTGGCTATGCCAAGTGTTTCATCATCATTGCTGATT
ATAGGAAGGACTCGAAGAACCTTGGCGGCCACGAGGTGAAAGGAATCCCCAATCGATGTCATCCCCATGGTGTACATCTC
AGTGTCCAGGGCCCTGGCCAGCATGTTTGGCAGCGTGGCCGAGCTGTGCATGGCCAAGTGCAAGGTGGAACCCATGGGGA
CGGATAATGGGAACTTTCTGTTGGACTGGAAGTTTGACCAGGTGCACAAATGAAGTGAAGTGAACACAGCCATCAAAATG
AGCTCAGGAGTTGTGGACATGGTTCTATTTATCAGCATGGCTGAAAGAGTCTACTTTGGCATGGAAGATGGCTCAGTCAA
CATGAGAGAGAGA

Alignment

ORF - retro_mdom_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.15 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLSDLDRHPELDLAIDGADEVDADLNLIKGGGGCLTQEKIVAGYAKRFIVIADYRKDSKNLGEHWVKGVP
          P...L..HP.LDLAID.ADEV...LNLIKGGGGCLTQEK.VAGYAK.FI.IADYRKDSKNLG.H.VKG.P
Retrocopy PAEWLTQHPGLDLAIDDADEVVTNLNLIKGGGGCLTQEKMVAGYAKCFIIIADYRKDSKNLGGHEVKGIP

Parental  -IEVIPMAYVPVARALARMFGGVAELRMAERKAGPVVTDNGNFLLDWKFDRVHPWSEVNTAIKMIPGVVD
          .I.VIPM.Y..V.RALA.MFG.VAEL.MA..K..P..TDNGNFLLDWKFD.VH..SEVNTAIKM..GVVD
Retrocopy >IDVIPMVYISVSRALASMFGSVAELCMAKCKVEPMGTDNGNFLLDWKFDQVHK*SEVNTAIKMSSGVVD

Parental  TGLFINMAERVYFGMEDGSVSVRER
          ..LFI.MAERVYFGMEDGSV..RER
Retrocopy MVLFISMAERVYFGMEDGSVNMRER

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_320 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_320 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002866	1 retrocopy	retro_btau_1373,
Equus caballus	ENSECAG00000011754	1 retrocopy	retro_ecab_645,
Macropus eugenii	ENSMEUG00000008256	1 retrocopy	retro_meug_1506,
Microcebus murinus	ENSMICG00000006462	1 retrocopy	retro_mmur_722,
Myotis lucifugus	ENSMLUG00000005384	1 retrocopy	retro_mluc_1129,
Monodelphis domestica	ENSMODG00000009649	1 retrocopy	retro_mdom_320 ,
Oryctolagus cuniculus	ENSOCUG00000006840	3 retrocopies	retro_ocun_1541, retro_ocun_1708, retro_ocun_1709,
Otolemur garnettii	ENSOGAG00000034178	2 retrocopies	retro_ogar_1218, retro_ogar_518,
Tarsius syrichta	ENSTSYG00000006406	8 retrocopies	retro_tsyr_1081, retro_tsyr_1088, retro_tsyr_1902, retro_tsyr_2028, retro_tsyr_393, retro_tsyr_709, retro_tsyr_725, retro_tsyr_994,
Tursiops truncatus	ENSTTRG00000000876	2 retrocopies	retro_ttru_1175, retro_ttru_799,