RetrogeneDB ID: retro_mdom_1080

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:16632641..16633393(-)
• Located in intron of: ENSMODG00000025406

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008227
• Aliases: None
• Description: None

Sequence

>retro_mdom_1080
CAACTAACACAAGACTTTGATGTGATAAGAGTGCTTTAAAGAAATCAAAAGCAGAACTCATGGAACTTAGTGAAGTTAAA
ACTAAAAATCAGCTCTCTAAGCAAATCCCTCCCTAACGTAACAGATGAATATAAAAAATGGAGTAAAAAACAGATCCATC
TATATTAGAGGTTTTCCAACAGATGCAACCTTTGATGATATAAAAGAATGGCTAGAAGGTAAAAGTCAAGTACCAAATAT
TCAGATGAGGAGAACAATACATAAAACATTTAAGGGCTTAATATTTGCTGTGATTGATAGTGTTGCATCTGTCAAAAAAT
TATAGAAAGCTCTGGACAAAAATATAAAAAAGTGCTGATATTGTTTAAGGAAAAAATAGTTTCCTTAAAAATCTAAAGAA
AGCAAGATAGAGTAGAAGGTAAAGCAAAAGCTAAATAAGTGCAAGAAGTAAAACAGAAGCAAGCAGAAAATACCAAATTG
AAATTCCTGGAAGAAAAAAGTGGATGTTTGCTTAAAATTTCCGGTGATTCAGATGACCAAACCAATAGAGAAAATCTTCA
ACATTTTTCTTTAATCATGGAGAAATAAAGTAGATAGACTTCCTCAAAGAAGCAAAAGAGGAAATAATCCTTTTTAAAGA
AAAGGCAAAAGAAAAACTGGGAAAAGTCAATGACATAAATGTTGAACTTTTAAAATTAAGAAACAAATATGTAACATGAT
AAGTATTGTAAGAAGAGATGGAGAAAGAAAGT

Alignment

ORF - retro_mdom_1080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.16 %
• Parental protein coverage: 61.48 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KLTKDFDVIR-SALKKSKAELMEVSEDKT-KIRRSPSKPLPEVTDEYK-NEVKNRSIYVKGFPTDATLDD
          .LT.DFDVIR.SALKKSKAELME.SE.KT.KI..S.SK.LP.VTDEYK.N.VKNRSIY..GFPTDAT.DD
Retrocopy QLTQDFDVIR<SALKKSKAELMELSEVKT>KIS-SLSKSLPNVTDEYK>NGVKNRSIYIRGFPTDATFDD

Parental  IKEWLEGKGQVQNIQMRRTLHKAFKGSIFAVFDSVESAKKF-IETPGQKYKDTELLILFKEDYFAKK---
          IKEWLEGK.QV.NIQMRRT.HK.FKG.IFAV.DSV.S.KK..IE..GQKYK....LILFKE.....K...
Retrocopy IKEWLEGKSQVPNIQMRRTIHKTFKGLIFAVIDSVASVKKL<IESSGQKYK--KVLILFKEKIVSLKI*R

Parental  NEERKQNKVEAK--AKAKQEQEEKQKQAEEAELASLLFLFSKELDDQTCREDLH-TLFSNHGEIKWIDFI
          ...R...K..AK.....KQ.Q.E..K.....E....L...S...DDQT.RE.L..T.F.NHGEIK.IDF.
Retrocopy KQDRVEGKAKAK*VQEVKQKQAENTKLKFLEEKSGCLLKISGDSDDQTNRENLQ<TFFFNHGEIK*IDFL

Parental  RGAKEGIILFKEKAKEALEKANEANSGNLKLRNKDVTWEVLEGETEKEA
          ..AKE.IILFKEKAKE.L.K.N..N...LKLRNK.VT..VL..E.EKE.
Retrocopy KEAKEEIILFKEKAKEKLGKVNDINVELLKLRNKYVT**VL*EEMEKES

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_1080 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1080 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 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007763	5 retrocopies	retro_chof_1125, retro_chof_1292, retro_chof_1380, retro_chof_185, retro_chof_2593,
Dasypus novemcinctus	ENSDNOG00000013450	1 retrocopy	retro_dnov_2038,
Echinops telfairi	ENSETEG00000004614	1 retrocopy	retro_etel_2056,
Homo sapiens	ENSG00000138385	1 retrocopy	retro_hsap_448,
Gorilla gorilla	ENSGGOG00000011507	3 retrocopies	retro_ggor_2914, retro_ggor_434, retro_ggor_791,
Gorilla gorilla	ENSGGOG00000023471	4 retrocopies	retro_ggor_2834, retro_ggor_2915, retro_ggor_433, retro_ggor_792,
Loxodonta africana	ENSLAFG00000000867	3 retrocopies	retro_lafr_698, retro_lafr_745, retro_lafr_982,
Macropus eugenii	ENSMEUG00000001650	1 retrocopy	retro_meug_1908,
Myotis lucifugus	ENSMLUG00000016316	1 retrocopy	retro_mluc_2493,
Macaca mulatta	ENSMMUG00000023051	2 retrocopies	retro_mmul_1153, retro_mmul_529,
Monodelphis domestica	ENSMODG00000008227	1 retrocopy	retro_mdom_1080 ,
Nomascus leucogenys	ENSNLEG00000004958	3 retrocopies	retro_nleu_1039, retro_nleu_177, retro_nleu_3011,
Otolemur garnettii	ENSOGAG00000029768	1 retrocopy	retro_ogar_1642,
Pongo abelii	ENSPPYG00000012919	3 retrocopies	retro_pabe_3408, retro_pabe_3641, retro_pabe_424,
Pan troglodytes	ENSPTRG00000012620	1 retrocopy	retro_ptro_2509,
Rattus norvegicus	ENSRNOG00000007998	1 retrocopy	retro_rnor_405,
Tupaia belangeri	ENSTBEG00000009056	4 retrocopies	retro_tbel_1065, retro_tbel_1269, retro_tbel_3318, retro_tbel_4012,
Tursiops truncatus	ENSTTRG00000002152	2 retrocopies	retro_ttru_1926, retro_ttru_466,