RetrogeneDB ID: retro_mdom_981

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:114688840..114689592(+)
• Located in intron of: ENSMODG00000003445

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011916
• Aliases: None
• Description: None

Sequence

>retro_mdom_981
CATTTCAATTCCAGTGCAATACAACATGCCACTGCTTTGACTATCTTTCCTTGCCACCTGTCCCTGGCCAACAACCCCAG
CCACCATGGAGGACATTAACAAATACAGCAGCATTAAGTTCTCCAGTGGCTCCAAAGTCAACATAAACAAGAACAAGCAG
GATGACAATAAAATATTTATTAAAAGGCCAAACTGGGACATGAACAAGAAAGATCTGACTGAGTACCTGTCTCATTTGGG
AGAGGTTGTAGATTATAAAATTAAGACAGATCCAGTCACTGGAAGATCAGGGGAATTTGGATTTGTACTTTTCAAAGATG
GTGCCAATGTTGATGATATCCTAGAACTTAAAAAACATAAACTGAATGGCAAGGTGAGAGACTCCTAAAGGGTTAAAACT
TTTAAAGGAAAAGAACCCCTCAAAAAAGTATTTGTGGGTGATCTAAACCCAAAAAACCTGAGGGACAAATCAAAGAATAT
TTTGGAGTACTTGGAAAGATTAAGAATATTGAATTTTCTATGGACAGCAATAACAAATGAAAGAAGGAGATTCTGTTTTA
TCATATATACAGATAAAGAACTAGGAAAGAATTTTTTAGAAAGTAGATTATCATCAAATTGATTCTGGAAAGTATGAAAT
AAAAATTGCCCAGATCGAAAAGGCACATAGTTAGCAAAAACAACAACCAAAAGGAGAAACATCCATTGTGACTAGTGGCC
AAGGTGGAACTAGGAGTCATGGCCAAGATCAA

Alignment

ORF - retro_mdom_981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.82 %
• Parental protein coverage: 60.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HFKSGSIHRAAAATPSPRHLPPADSP-AAMEDVNEYSNMEEFAEGSKINASKNQQDDGKMFIGGLSWDTS
          HF.S..I..A.A.T..P.HL..A..P.A.MED.N.YS....F..GSK.N..KN.QDD.K.FI....WD..
Retrocopy HFNSSAIQHATALTIFPCHLSLANNP>ATMEDINKYSSIK-FSSGSKVNINKNKQDDNKIFIKRPNWDMN

Parental  KKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKE
          KKDLTEYLS..GEVVD..IKTDPVTGRS..FGFVLFKD.A.VD..LELK.HKL.GK..D..R.K..KGKE
Retrocopy KKDLTEYLSHLGEVVDYKIKTDPVTGRSGEFGFVLFKDGANVDDILELKKHKLNGKVRDS*RVKTFKGKE

Parental  PPKKVFVGGLSPDT-SEEQIKEYFGAFGEIENIELPMDTK-TNERRGFCFITYTDEEPVKKLLENR-YHQ
          P.KKVFVG.L.P....E.QIKEYFG..G.I.NIE..MD...TNERR.FCFI.YTD.E..K..LE.R.YHQ
Retrocopy PLKKVFVGDLNPKN<PEGQIKEYFGVLGKIKNIEFSMDSN>TNERRRFCFIIYTDKELGKNFLESR>YHQ

Parental  IGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQ
          I.SGK.EIK.AQ.......Q.QQ.KG.......G.GGTR..G..Q
Retrocopy IDSGKYEIKIAQIEKAHS*QKQQPKGETSIVTSGQGGTRSHGQDQ

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_981 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_981 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 11 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981 ,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Sarcophilus harrisii	ENSSHAG00000013616	3 retrocopies	retro_shar_297, retro_shar_527, retro_shar_625,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tupaia belangeri	ENSTBEG00000002817	7 retrocopies	retro_tbel_2079, retro_tbel_2283, retro_tbel_2608, retro_tbel_2874, retro_tbel_3344, retro_tbel_4302, retro_tbel_4405,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,