RetrogeneDB ID: retro_mdom_14

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:53446057..53447806(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000014335
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018546
• Aliases: None
• Description: None

Sequence

>retro_mdom_14
GGTTTGAGTGGCCCCCTGGCAGCACAGGAGACCCAGGCCCAGAGCTCCTGCAAGAAAGATTCACCTCTCTGCTTCATGAT
TAAGACCGGAGTGATTGGAGCCAGCACAAGCCAAAGAGGCAACAAAGTGAAAAAGTTGCCAGAATTTCCTGGCTCTAAAA
TGCGGAACCCCAGAGGAGAATCTGAGTCAGAGGCAAGGGCATATGGCAAACAACAGAGCCAGAAACCAGCTAAGTCGGCA
ATGGAAGAAACGGTTAAAAAAGCAGAGAGGTATTCTAAAGAGGGAGCAAAAAGGAGCGGCACCTTGAAAACATCTACTGA
AAAGGCCACCGAAAGGAAAGTACCTGTGATTGATTGGGATGCAATTAGACAAAGCCACCTGCAATACATTAAAAATAAGT
GGGGAAGCCTACCACCTGTCAAAAAAGATTTTTATGTTGAATCAGCGAGAACAAAATCAATGTTACAATCAGAAGCAGAC
AGGTGGCGCAAAGAAAACAATAATGTAACTTGTGATGATTTAAAAACCAATGAAAAAAGATCTATTCCGCACCCTGTCTG
CCAATTCGAAGATGCATTTCATCAATATCCGGAAGTTATGGAAAATATCAGGAAGGTAGGTTTCAGCAAACCCACGCCAA
TACAATCACAGGCATGGCCAATCATATTGAAAGGTATTGACCTAATCAGTATTGCCCAAACAGGTACTGGGAAAACATTA
GCGTACCTGATGCCAGGCTTTATTCATCTTGACCACCAGCCAGTAGCCAGGGAGGAGAGGAGGGGGCCTGGTATGCTAGT
GCTCACACCAACCAGAGAATTAGCGATTCAAGTTGACAATGAATGTAAGAAATACACTTATAAGGGAATTAAAAGCATGT
GTATATATGGGGGAGACAAAAGTGGTCCAACTGAGCATATTCCCAGGGGTATAGATATTATCATTGCCACCCCAGGCCGA
CTTAGCGACCTGCAGATGAACGACCTCGTCAATCTTAATAGTATTACATACGTGGTTCTAGATGAGGCTGATAAGATGTT
GGATATGGGGTTTGAGCCTCAAATAATGAAAATTTTATCAGATATACGGCCAGATAGGCAAACGGTAATGACCAGCGCTA
CCTGGCCCGATATTGTCCGTCATTTGTCACAAAAATACCTAAAAGATCCAATGATAGTTTATGTTGGCACCTTGGATCTA
ACCACCGTGAACACCATAAAACAGAAAATCATCGTAACCACTGAAGAAGAAAAACGAGTTTTGCTACGTTCTTTCATCGA
TTCGTTGATGCCTGAACATAAAGTAATTATTTTTGTGAGCAGAAAACTTATTGCTGATGATATATCCAGTGACCTGAGCA
TTAAGGGCATACCTGTGCAGTCACTCCATGGTAGTCGAGAACAAGATGACCGAGACCAAGCATTAGAGGAATTTAAAAAA
GGAATAGTGAAAATATTAATAGCTACAGATCTGGCATCACGAGGTATCGACGTCCTCGATGTCACTCATGTTTTTAACTT
TGATTTTCCTCAAAACATTGAAGAATACATCCATAGAATTGGACGTACGGGACGAGCTGGACAAAGTGGGTCATCGATCA
CTTTACTCACCAAAGGCGACTGGAGCGTTGCGGGGGAGCTAATTAACATCTTACAGCGGGCCAACCAAGAGGTCCCCCGT
GAGCTTGCATCAATGGCTAGGCAATATAAGCAGTACAAACACAGAAAGAACGAGGAAAAGAAGTTAAGA

Alignment

ORF - retro_mdom_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.21 %
• Parental protein coverage: 90.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSRGPSGVLEYRARSSCFREAPLCFKLDSSVVGAVIGRGGTKIKEIQESTGSKIQIIKGDSESETRIYGN
          G..GP....E..A.SSC....PLCF.....V.GA.....G.K.K...E..GSK.....G.SESE.R.YG.
Retrocopy GLSGPLAAQETQAQSSCKKDSPLCFMIKTGVIGASTSQRGNKVKKLPEFPGSKMRNPRGESESEARAYGK

Parental  KENQKSAKLMIEEIVKKIEKYSKEDTKIGNTLKSSCNENGPDKKVPVIDWEAIKQDHLHYIKTKWDGLPP
          ...QK.AK...EE.VKK.E.YSKE..K...TLK.S..E.....KVPVIDW.AI.Q.HL.YIK.KW..LPP
Retrocopy QQSQKPAKSAMEETVKKAERYSKEGAKRSGTLKTS-TEKATERKVPVIDWDAIRQSHLQYIKNKWGSLPP

Parental  IKKDFYIESSKTKLMSQTQVDKWREENNNIMCDDLRENEKRIIPNPVCTFEDAFDHYPDVMANIKKVGFT
          .KKDFY.ES..TK.M.Q...D.WR.ENNN..CDDL..NEKR.IP.PVC.FEDAF..YP.VM.NI.KVGF.
Retrocopy VKKDFYVESARTKSMLQSEADRWRKENNNVTCDDLKTNEKRSIPHPVCQFEDAFHQYPEVMENIRKVGFS

Parental  RPTPIQSQAWPIILKGIDLIGIAQTGTGKTLAYLMPGFIHLDLQPETREKRDGPGMLVLTPTRELALQVE
          .PTPIQSQAWPIILKGIDLI.IAQTGTGKTLAYLMPGFIHLD.QP..RE.R.GPGMLVLTPTRELA.QV.
Retrocopy KPTPIQSQAWPIILKGIDLISIAQTGTGKTLAYLMPGFIHLDHQPVAREERRGPGMLVLTPTRELAIQVD

Parental  SECKKYTYKGIKSICIYGGGDRRGQIEHVTKGVDIVIATPGRLNDLQMNEFINLNSITYLVLDEADKMLD
          .ECKKYTYKGIKS.CIYGG.D..G..EH...G.DI.IATPGRL.DLQMN...NLNSITY.VLDEADKMLD
Retrocopy NECKKYTYKGIKSMCIYGG-DKSGPTEHIPRGIDIIIATPGRLSDLQMNDLVNLNSITYVVLDEADKMLD

Parental  MGFEPQIMKILLDVRPDRQTIMTSATWPDAVRRLSQKYLNDPMIVYVGTLDLAAVNTVKQKIIITTEQEK
          MGFEPQIMKIL.D.RPDRQT.MTSATWPD.VR.LSQKYL.DPMIVYVGTLDL..VNT.KQKII.TTE.EK
Retrocopy MGFEPQIMKILSDIRPDRQTVMTSATWPDIVRHLSQKYLKDPMIVYVGTLDLTTVNTIKQKIIVTTEEEK

Parental  PALIHSFIDSMKPEDKVIIFVGRKLIADDISSDLSIKGLPVQSLHGNREQSDRERALNEFKTGIVRILIA
          ..L..SFIDS..PE.KVIIFV.RKLIADDISSDLSIKG.PVQSLHG.REQ.DR..AL.EFK.GIV.ILIA
Retrocopy RVLLRSFIDSLMPEHKVIIFVSRKLIADDISSDLSIKGIPVQSLHGSREQDDRDQALEEFKKGIVKILIA

Parental  TDLASRGLDVLDITHVFNFDFPRNLEEYVHRVGRTGRAGHTGESITLLTRNDWKIAGELINILERANQEI
          TDLASRG.DVLD.THVFNFDFP.N.EEY.HR.GRTGRAG..G.SITLLT..DW..AGELINIL.RANQE.
Retrocopy TDLASRGIDVLDVTHVFNFDFPQNIEEYIHRIGRTGRAGQSGSSITLLTKGDWSVAGELINILQRANQEV

Parental  PNELILMAERYKQHKQKKDEERNM
          P.EL..MA..YKQ.K..K.EE...
Retrocopy PRELASMARQYKQYKHRKNEEKKL

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_14 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_14 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14 ,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061, retro_ocun_227,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,