RetrogeneDB ID: retro_mdom_1650

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:46787126..46787922(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000007541
• Aliases: None
• Description: None

Sequence

>retro_mdom_1650
ATAGTGGGCAACAATCCAGGAGTGACTCTGGGACAGTCACATCTATCTCACCAGGATTTGACCACTTTGGATGTTACCAA
GTTTCCTTGGTAACTTTCACATGAAGTTATCAGCAGAGAAGCCACAATCAATATAGGTACAATTGGTCATGTAGCACATG
GAAAGTCAAGAGTAGTAAAAGCTATTTCTGGAGTTCACACTGTCCAATTAAAAAATGAGCTGGAAAAAATATACCATTTA
ATTGGAATATGTTAAGATTTACCAACTTAATGACCCAAGTTGTTCTCAGCCAGAATGCTACAGATATTGTGGAAGTAGCA
CACCTAATGAATTTCCTACAGATGTTCCAGGAACTAAAGGAAAGTTCAAATTAGTCAGACATGTCTTCCTTGTGGATTGT
CCTGTTCACAATATTTTGATGGCTACCATGCTGAACGGTGCAGCAGTAATGGATGCAGCTTTGTTATTAATAGTTGGCAA
TGAGTCTTGTCCTCAGCCTCAGACTTCTGAGCACCTAGCTGCCATTGAAATCATGAAATTGAAACACATTCTGATTCTAC
AGAATAGAATTGATTTGGTGAAGGAAAATCAGGCTAAGGAACAATATGAACAAATCCTTGCATTTGTACAAGGTACAGTT
GCAGAGGGAACTCCTATTATTCTAATTTCTGTTCAGCTGAAGTATAATATTGCAGTTGTTTGTGAATATATAGTAAAGAA
AATTCCAGTACCCTCAAGGGACTTTACTTCAGAGCCCAGAATTATTTTTATTCAGTCTTTTGACTTCAAGAAGCCT

Alignment

ORF - retro_mdom_1650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 56.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGDEPGVTLGQPHLSRQDLTTLDVTKLTP-LSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRF
          ..G..PGVTLGQ.HLS.QDLTTLDVTK....LSHEVISR.ATINIGTIGHVAHGKS.VVKAISGVHTV..
Retrocopy IVGNNPGVTLGQSHLSHQDLTTLDVTKFPW*LSHEVISREATINIGTIGHVAHGKSRVVKAISGVHTVQL

Parental  KNELE-RNI-TIKLGYANAKIYQLDDPSCSRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPG
          KNELE..NI.TI.L.Y...KIYQL.DPSCS.PECYR.CGSSTP.EFPTD.PGTKG.FKLVRHV..VDCP.
Retrocopy KNELE<KNI<TI*LEYV--KIYQLNDPSCSQPECYRYCGSSTPNEFPTDVPGTKGKFKLVRHVFLVDCPV

Parental  HDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQI
          H.ILMATMLNGAAVMDAALLLI.GNESCPQPQTSEHLAAIEIMKLKHILILQN.IDLVKE.QAKEQYEQI
Retrocopy HNILMATMLNGAAVMDAALLLIVGNESCPQPQTSEHLAAIEIMKLKHILILQNRIDLVKENQAKEQYEQI

Parental  LAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKP
          LAFVQGTVAEG.PII.IS.QLKYNI.VVCEYIVKKIPVP.RDFTSEPR.I.I.SFD..KP
Retrocopy LAFVQGTVAEGTPIILISVQLKYNIAVVCEYIVKKIPVPSRDFTSEPRIIFIQSFDFKKP

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_1650 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1650 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650 , retro_mdom_732,
Mus musculus	ENSMUSG00000035150	2 retrocopies	retro_mmus_1408, retro_mmus_3433,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,