RetrogeneDB ID: retro_mdom_1666

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:96924966..96925997(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008402
• Aliases: None
• Description: None

Sequence

>retro_mdom_1666
GGGAAAGGAGACAAAAAGATTAAAGCACTTTATACAGCCTACACCACCAGGGTTTCAGTCCTAGATAGTGACTCTGAGCA
CATATTGAGTATCAGGGCAAATCCTGAAACAATTGGAGAAACCCTCAAGAAAATTATCCCTACTTCAGAAGTGTAAAACA
CTATAAAGGAAAAGACTTTTAATTGTGATTATAAGATTATTAATTCACCAGAGTCTGGCAGGAGGAATTATTGGGGTCAG
AGGATAAAGTCAAAGATCTTTGAGAGAATACTTGGACAACAATCAAGTTTTTCCTGGGATGCTGTCTTAAATTCACTGAT
AGAGTTGTTCTGATTGGTGGAAAGTCCGATAGGATTATGGAGTGCATAAAGATCATATTAGATCTTATATCTGAATTTCC
TATCAAAGGACATACAAAACCCTATAATCACAATTTTTATAATGAAACCTATCAGTATGTTATTTTCACAATGATGATTG
GTGAGTAATGAAGATATATTGTAGGATTTCCCATGAAGGGAAGAGGGGGCTTTGATAGAATGTCCCCTTGATGATGGTGG
GCATCCTATGCCCCCATTTAGAAGAGAATATAATGAAATGAGCTCTCTTGGAAAACTCTGGCCACCTCCTTTTTGGCCAT
GGTGGAGGCGTAAAATGCAAAGCTTGAACTCTTTCTATTCTACCACCATTGCCTAAAAGAAGAGGTATTATAGTTTATGA
CAGAAGAGGAATTCCTAAAGAATTATGATGATGCCTTAGTTGTTTTTGGTGTGGGTAAGACTGGGGACTCTACATTAGAT
ATATAGAGTCTTTCTGAATGGCAGATGGCTTATGAACTGTAGGGTGATGCTGGATATAATTTTTCCTCTGCAAGAGGCCA
TGTCTCAAATAATGATCTTAGTGAACCCATTATTACAACACAAAGAACTATTCCCAAAGATTTGACTGGATCTATTACTG
GCAAAAGTGGTCAGTGAATTAAACAAATGCCTTATCAATCCAGAGCATCAATCACAGTTAATAAGCTTTTG

Alignment

ORF - retro_mdom_1666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.67 %
• Parental protein coverage: 78.05 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GKGGKNIKALRTDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLE-EYQHYKGSDF-DCE-LRL
          GKG.K.IKAL.T.Y...VSV.DS...E.ILSI.A..ETIGE.LKKIIPT.E....HYKG.DF..C...RL
Retrocopy GKGDKKIKALYTAYTTRVSVLDSDS-EHILSIRANPETIGETLKKIIPTSE<SVKHYKGKDF>NCD>IRL

Parental  LIHQSLAGG-IIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISESPI
          LIHQSLAGG...G....K.K.L.ENT.TTIK.F..CC...TDRVVLIGGK.DR..ECIKIILDLISE.PI
Retrocopy LIHQSLAGG>LLGSED-KVKDL*ENTWTTIKFFLGCCLKFTDRVVLIGGKSDRIMECIKIILDLISEFPI

Parental  KGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPP-GRGGRPMPPSRRDYDDMSPRR
          KG...PY..NFY.ETY.Y..FTMM........VGFPM.GRGGFDRM.P...GG.PMPP.RR.Y..MS...
Retrocopy KGHTKPYNHNFYNETYQYVIFTMMIGE**RYIVGFPMKGRGGFDRMSP>DDGGHPMPPFRREYNEMSSLG

Parental  GPPPPP-PGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGD-RYDGMVGFSADETWDSAIDTWSPS
          ...PPP..G.GG.....A..L...PP.P.R.G....YDRRG.P.....D..V.F....T.DS..D..S.S
Retrocopy KLWPPP>FGHGGGVKCKA*TLSILPPLPKRRG-IIVYDRRGIPKE>YDDALVVFGVGKTGDSTLDI*SLS

Parental  EWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE
          EWQMAYE..G..GY..S.A.G..S..DL..PIITTQ.TIPKDL.GSI.GK.GQ.IKQ....S.ASI....
Retrocopy EWQMAYEL*GDAGYNFSSARGHVSNNDLSEPIITTQRTIPKDLTGSITGKSGQ*IKQMPYQSRASITVNK

Parental  PL
          .L
Retrocopy LL

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_1666 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1666 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 22 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Choloepus hoffmanni	ENSCHOG00000010832	2 retrocopies	retro_chof_1023, retro_chof_1589,
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macropus eugenii	ENSMEUG00000006975	3 retrocopies	retro_meug_271, retro_meug_357, retro_meug_484,
Microcebus murinus	ENSMICG00000015780	3 retrocopies	retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666 ,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Sus scrofa	ENSSSCG00000022760	1 retrocopy	retro_sscr_437,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,