RetrogeneDB ID: retro_mdom_1364

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:152936129..152937542(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010436
• Aliases: None
• Description: None

Sequence

>retro_mdom_1364
GTTAAGGTTTCCACTAAATCCAATAGTACTGCTACTTCCCAGAACAAAACAACTTTTCAGTGTTCTGGGAAAAAGCAAGT
TGACTTTATCCAAAACAAGGAGAAAGAAGCCATTGTTAGAACCTTTTTCTAACCTACTATCTAAGTTACTATCTAAAGAG
AGCCTAATAAAGATAGTACCTCTACCAATGCCAGTACTACCAAATGTCAAGATAAACCTGAATTCTGGTAAAAAAGAAAA
TAAAGCACAATCAAAATGTAGGACTTCTGGAGCGGCAACTACTCATATTTCTGAAGTAAAACCTGCTTCATCTTTCAGTA
CCAAATTCAGGGAGGATTCCAAAATTGGTGATAAGAGAAGATACACTTGAATAAAAGTGCCAATTAGTACAGAAGAACTG
CCTTAACCAAAGAATCAGCAGAAGAGAAAAGAGCTTGTTTGGTTGAGTGGCAAAATGACAAAAGAAGAGTAATTAAAAGA
TCATCTACAACTGGTCTGCCTGTTCCACCTGCTCCACCCAACATGGAACTGCCAAAAGAAAAACCAGTTGAATCTTTCTG
GACTACCATTGCAGAAGATGAACAAAGATTATTCACTGATAAACTTAACAAAATATTTTTTGAATATTTGAACTTAATTA
ATAAGGGATGTCCATGAGGAGAAGTACTTTTAACACTAAAAGAGCTCATTGTAAAAATTCCAGATGCCAAGAAACTTATT
AAGTATCGGGTATGCCTTGCATGCCTTGAACCAATTACAAGCCCTATTGAAAATATCATAGCAATATATGAAGAAGCCAT
TCTTGCTGGAGCTCAGCCTATGGAAGAAATGCAACATGCGCTTGCAGATATCCTAACAATGAAGAGTCAAGTGAAGGGTA
ATGATGGGGAGAATATTGATGAGGTTTGTTCGGCTAATGAAGAGGCCAAAAAAATATGTGATGAACTTATACATCAGGAT
AAAGTTGATGTAGATGGGACATCAACAGAGGAAAATTCAGAATCAAAAGATAAAGATCATGAAACAAGGAATGTAAAACT
ACAGATGTTTGAAAGAGAGCAAGAGGATAAAGCAGAAGATTCAACAAGTGTTTTAGAGACTCCTGATAAGGAAACCAGCG
GGTCTTATGTCATTAAATATAATGTGTCAACTACTCCATCTTTGCCAAGTGTGAAACAGAAGATGAATTTTGATGAAAAT
ACTGCTTCATTTAAAGACGTGAAGTTTCTGACACCAGTGAGGCATTCTCGACGTCTGCAGGAGAAGTTTTGTAAATGACC
AGATATGTTAAATGATCATTATCCCTGTGTTTCTTCACTGGAACAGTTAGCAGAACTGGGAAGTGAAACCACTGCCTATA
TATGCCGTCCAAATACTGCATTATATACAACTTCCCTTGAAGAAGAAGCAAAA

Alignment

ORF - retro_mdom_1364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.02 %
• Parental protein coverage: 66.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSVSTKSNSTTTSQNKTAFQHSGKKQVDFIQN-KEKEAIVRNSTNVT---IRREPNKKIVPLSKPVLPNV
          V.VSTKSNST.TSQNKT.FQ.SGKKQVDFIQN...K........N........E...KIVPL..PVLPNV
Retrocopy VKVSTKSNSTATSQNKTTFQCSGKKQVDFIQN>RRKKPLLEPFSNLLSKLLSKESLIKIVPLPMPVLPNV

Parental  KTNLNSGKKENEVQSKCRTSGAATTHVSEAKPASSFSTRFREDSKIVDKRRYTLTKAPISTG-RTALTKE
          K.NLNSGKKEN..QSKCRTSGAATTH.SE.KPASSFST.FREDSKI.DKRRYT..K.PIST..RTALTKE
Retrocopy KINLNSGKKENKAQSKCRTSGAATTHISEVKPASSFSTKFREDSKIGDKRRYT*IKVPISTE<RTALTKE

Parental  SAEERRARLVEWQNDKRRVIKRSSTTGLTVPPAPPAPSNIELPKEKPLESFWTTIAEEDEQRLFTDKVNK
          SAEE.RA.LVEWQNDKRRVIKRSSTTGL.VPPAPP...N.ELPKEKP.ESFWTTIAE.DEQRLFTDK.NK
Retrocopy SAEEKRACLVEWQNDKRRVIKRSSTTGLPVPPAPP---NMELPKEKPVESFWTTIAE-DEQRLFTDKLNK

Parental  IFSEYLNLINKGCPREEVLLTLKELIVKIPDAKKLVKYWVCLARLEPITSPIENIIAIYEEAILAGAQPM
          IF.EYLNLINKGCP..EVLLTLKELIVKIPDAKKL.KY.VCLA.LEPITSPIENIIAIYEEAILAGAQPM
Retrocopy IFFEYLNLINKGCP*GEVLLTLKELIVKIPDAKKLIKYRVCLACLEPITSPIENIIAIYEEAILAGAQPM

Parental  EEMRHALADILTMKSQVKGNDGENVDEVCSANEEIKKLCDEVLNQDKVDVDEASAEENSESKDKDHNTKN
          EEM.HALADILTMKSQVKGNDGEN.DEVCSANEE.KK.CDE...QDKVDVD..S.EENSESKDKDH.T.N
Retrocopy EEMQHALADILTMKSQVKGNDGENIDEVCSANEEAKKICDELIHQDKVDVDGTSTEENSESKDKDHETRN

Parental  VKLQMVEREQEDKAEDSTSVLETPDKETSGSYVIKYNVSTTPYLQSVKKKMNFDENSASFKDLKFLTPVR
          VKLQM.EREQEDKAEDSTSVLETPDKETSGSYVIKYNVSTTP.L.SVK.KMNFDEN.ASFKD.KFLTPVR
Retrocopy VKLQMFEREQEDKAEDSTSVLETPDKETSGSYVIKYNVSTTPSLPSVKQKMNFDENTASFKDVKFLTPVR

Parental  RSRRLQEKFCKLPDMLKDHYPCVSSLEQLAELGSESSAYICRPNTALCTTSLEEEIK
          .SRRLQEKFCK.PDML.DHYPCVSSLEQLAELGSE..AYICRPNTAL.TTSLEEE.K
Retrocopy HSRRLQEKFCK*PDMLNDHYPCVSSLEQLAELGSETTAYICRPNTALYTTSLEEEAK

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_1364 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1364 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968,
Choloepus hoffmanni	ENSCHOG00000009905	2 retrocopies	retro_chof_1493, retro_chof_973,
Cavia porcellus	ENSCPOG00000012382	1 retrocopy	retro_cpor_171,
Felis catus	ENSFCAG00000010021	1 retrocopy	retro_fcat_1770,
Myotis lucifugus	ENSMLUG00000000132	1 retrocopy	retro_mluc_1515,
Monodelphis domestica	ENSMODG00000010436	1 retrocopy	retro_mdom_1364 ,
Mustela putorius furo	ENSMPUG00000017996	1 retrocopy	retro_mputfur_1270,
Mus musculus	ENSMUSG00000037725	1 retrocopy	retro_mmus_2651,
Otolemur garnettii	ENSOGAG00000008428	1 retrocopy	retro_ogar_1743,
Tupaia belangeri	ENSTBEG00000005807	1 retrocopy	retro_tbel_176,
Tursiops truncatus	ENSTTRG00000009624	2 retrocopies	retro_ttru_1491, retro_ttru_1741,