RetrogeneDB ID: retro_mdom_1323

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:11153144..11154099(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000021045
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017334
• Aliases: None
• Description: Ribose-phosphate pyrophosphokinase [Source:UniProtKB/TrEMBL;Acc:F6WVR9]

Sequence

>retro_mdom_1323
ATGCCCAACTTTGTGCTGTTCAGTGGCAGCTCAAACCAGGACTTGTCCCAGAAAGTGGCTGACAGGTTGGGGCTAGAACT
GGGCAATGTAGTCACTAAGAAATTCAGCAATCAGGAACCCAGTATAGAAATCGGTGAAAATGTGAGAGGGGAAGATGTCT
ACATTATCCAAAGCAGCTGTGGGGAAATGAATGATAACTTGATGGAACTTCTCATTATGACCAATGCTTGCAAAATTGCA
TCATCATCCAGGGTGATTGCGGGGATCCCATGTTTTCCATATGCCTGAGAAGATAAAAAAAGACAAGAGTTGTGCTCCAA
TTTCTGTAAAACTTGTGACTAATCTGCTTTCCATGGCTGGGACTGATCATATCATTACAATGGATCTCCATGCTTCTCAG
ATACAGGAATTTTTTAATATTCCAGTGGGTAATTTGTATGCAGAACCTACAGTTTTACAATGGATTCAAGAAAATATTGC
AGAATTTAGGAATTGTATCATTGTGTCTCCAGATGCTGGTGGAGCTAAAAGAGTGACATCGATTGTTGACACACTGAATG
TGGAGTTTGCTTTGATTCATAAAGAAAGAAAGAAGGCAAATGAAGTAGACAGGATGGTTTTGGTTGGTGACACGAAGGAT
GGTGTAGCCATCCTTGTGGATGACATGGCTGATACATGTGGCACAATATGCCATGCTGCAGATAAGTTACTGTCTGCTGG
AGTCACCAAATTTTATGCTATTCTGACTCATGGAATCTTCTCTGGGCCAACTATTTCCAGGATTAATAATGCGGCATTTG
AGGCTGTGGTGGTCACAAATACAATTCCACAAGAAGACAAAATGAAGCACTGATCTAAAATCTAGGCAATTGATATTTCA
ATGATACTGGCTGAAGCAATACAGAGAACACACAATGGTGAATCTGTATCTTACCTGTTCAGTCATGTTCCACTA

Alignment

ORF - retro_mdom_1323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPNIVLFSGSSHQDLSQKVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEINDNLMEL
          MPN.VLFSGSS.QDLSQKVADRLGLELG.VVTKKFSNQE.S.EIGE.VRGEDVYIIQS.CGE.NDNLMEL
Retrocopy MPNFVLFSGSSNQDLSQKVADRLGLELGNVVTKKFSNQEPSIEIGENVRGEDVYIIQSSCGEMNDNLMEL

Parental  LIMINACKIASSSRVTAVIPCFPYARQDKK-DKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFD
          LIM.NACKIASSSRV.A.IPCFPYA..DKK.DKS.APIS.KLV.N.LS.AG.DHIITMDLHASQIQ.FF.
Retrocopy LIMTNACKIASSSRVIAGIPCFPYA*EDKK>DKSCAPISVKLVTNLLSMAGTDHIITMDLHASQIQEFFN

Parental  IPVDNLYAEPAVLQWIRENIAEWRNCIIVSPDAGGAKRVTSIADRLNVEFALIHKERKKANEVDRMVLVG
          IPV.NLYAEP.VLQWI.ENIAE.RNCIIVSPDAGGAKRVTSI.D.LNVEFALIHKERKKANEVDRMVLVG
Retrocopy IPVGNLYAEPTVLQWIQENIAEFRNCIIVSPDAGGAKRVTSIVDTLNVEFALIHKERKKANEVDRMVLVG

Parental  DVKDRVAILVDDMADTCGTICHAADKLLSAGATKVYAILTHGIFSGPAISRINNAAFEAVVVTNTIPQED
          D.KD.VAILVDDMADTCGTICHAADKLLSAG.TK.YAILTHGIFSGP.ISRINNAAFEAVVVTNTIPQED
Retrocopy DTKDGVAILVDDMADTCGTICHAADKLLSAGVTKFYAILTHGIFSGPTISRINNAAFEAVVVTNTIPQED

Parental  KMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          KMKH.SKI..IDISMILAEAI.RTHNGESVSYLFSHVPL
Retrocopy KMKH*SKI*AIDISMILAEAIQRTHNGESVSYLFSHVPL

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_1323 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1323 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 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011662	2 retrocopies	retro_cfam_1037, retro_cfam_1433,
Callithrix jacchus	ENSCJAG00000003885	1 retrocopy	retro_cjac_364,
Cavia porcellus	ENSCPOG00000007206	1 retrocopy	retro_cpor_16,
Dipodomys ordii	ENSDORG00000007577	2 retrocopies	retro_dord_223, retro_dord_605,
Echinops telfairi	ENSETEG00000005166	2 retrocopies	retro_etel_1613, retro_etel_669,
Felis catus	ENSFCAG00000026323	1 retrocopy	retro_fcat_527,
Monodelphis domestica	ENSMODG00000009171	1 retrocopy	retro_mdom_1440,
Monodelphis domestica	ENSMODG00000017334	4 retrocopies	retro_mdom_1323 , retro_mdom_1359, retro_mdom_258, retro_mdom_834,
Otolemur garnettii	ENSOGAG00000016087	1 retrocopy	retro_ogar_1440,
Procavia capensis	ENSPCAG00000001197	2 retrocopies	retro_pcap_219, retro_pcap_292,
Pongo abelii	ENSPPYG00000020125	1 retrocopy	retro_pabe_3431,
Pteropus vampyrus	ENSPVAG00000009452	1 retrocopy	retro_pvam_1224,
Sorex araneus	ENSSARG00000007710	1 retrocopy	retro_sara_18,
Ictidomys tridecemlineatus	ENSSTOG00000006056	1 retrocopy	retro_itri_1668,
Tupaia belangeri	ENSTBEG00000009917	1 retrocopy	retro_tbel_1245,
Tursiops truncatus	ENSTTRG00000003226	1 retrocopy	retro_ttru_1494,