RetrogeneDB ID: retro_mdom_834

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:145539336..145540288(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006765
• 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_834
ATGCCCAACATCGTGCTGTTCAGCGGCAGCTCGCACCAGGACCTGTCCCAGAAAGTGGCGGACAGATTGGGACTAGAACT
GGGCAAGGTAGTCACTAAGAAATTCAGCAATCAGGAGACCAGTGTAGAAATCGGTGAAAGTGTGAGAGGGGAAGATGTCT
ACATTATCCAAAGTGGCTGTGGGGAAATTAATAACTTGATGGAACTTCTCATTATGATCAATGCTTGCAAAATTGCATCA
TCATCCAGGGTGACTGCAGTGATCCCATGTTTTCCATATGCCCGACAAGATAAAAAAGACAAGAGTCGTGCTCCAATTTC
TGCAAAACTTGTGGCTAATATGCTTTCCGTGGCTGGGGCTGATCATATCATTACAATGGATCTCCATGCTTCTCAGATAC
AGGGATTTTTTTGATATTCCAGTGGATAATTTGTATGCAGAACCTGCAGTCTTACAGTGGATTCGAGAAAATATTGCAGA
ATGGAGGAATTGTATCATTGTGTCTCCAGATGCTGGTAGAGCTAAAAGAGTGACATCAATTGCTGACAGACTGAATGTGG
AGTTTGCTTTGATTCATAAAGAAAGAAAGAAGGCAAATGAAGTAGACAGGATGGTTTTGGTTGGTGACGTGAAGGATCGT
GTAGCCATCCTTGTGGATGACATGGCTGATACATGTGGCACAATATGCCATGCTGCAGACAAGTTACTGTCTGCTGGAGC
CACCAAAGTTTATGCAATTCTGACTCATGGAATCTTCTCTGGGCCAGCTATTTCTAGGATTAATAATGCGGCATTTGAGG
CTGTGGTGGTCACAAATACAATTCCACAAGAAGACAAAATGAAGCACTGCTCTAAAATCCAGGTTATTGACATTTCAATG
ATACTGGCTGAAGCAATACGGAGAACACACAATGGTGAATCTGTATCTTATCTGTTCAGTCATGTTCCACTA

Alignment

ORF - retro_mdom_834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPNIVLFSGSSHQDLSQKVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEINDNLMEL
          MPNIVLFSGSSHQDLSQKVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEIN.NLMEL
Retrocopy MPNIVLFSGSSHQDLSQKVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEIN-NLMEL

Parental  LIMINACKIASSSRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFF-D
          LIMINACKIASSSRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFF.D
Retrocopy LIMINACKIASSSRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFF>D

Parental  IPVDNLYAEPAVLQWIRENIAEWRNCIIVSPDAGGAKRVTSIADRLNVEFALIHKERKKANEVDRMVLVG
          IPVDNLYAEPAVLQWIRENIAEWRNCIIVSPDAG.AKRVTSIADRLNVEFALIHKERKKANEVDRMVLVG
Retrocopy IPVDNLYAEPAVLQWIRENIAEWRNCIIVSPDAGRAKRVTSIADRLNVEFALIHKERKKANEVDRMVLVG

Parental  DVKDRVAILVDDMADTCGTICHAADKLLSAGATKVYAILTHGIFSGPAISRINNAAFEAVVVTNTIPQED
          DVKDRVAILVDDMADTCGTICHAADKLLSAGATKVYAILTHGIFSGPAISRINNAAFEAVVVTNTIPQED
Retrocopy DVKDRVAILVDDMADTCGTICHAADKLLSAGATKVYAILTHGIFSGPAISRINNAAFEAVVVTNTIPQED

Parental  KMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          KMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
Retrocopy KMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL

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_834 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_834 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,