RetrogeneDB ID: retro_mdom_1209

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:494072884..494073469(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003785
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011269
• Aliases: None
• Description: None

Sequence

>retro_mdom_1209
ATTGCATCTGGTAGCAGGACTAAAAACCTAGACTTCTGCCGAAAGTGGGACAAAGATGAATATGAGAAAGTTGCAGAGAA
ACGACTTGATTAAGAAAGAGAGAAAATTACAGAACACCAGTGAAGCCTGTCAAGCGGGAGCTCTTACGGCATAGGGATTA
CAAAGGTGATTTGGAGTCCAAGTTGGGAAAGACCATAGTTATCACCAAGACCACCCCACAGTTCCAAATCAGAGGGTATT
ACTGCAATATTTGTGACTCTGTAGTGAAAGACTGCATCAACTTCTTGGATCACATCAATGGCAAGAAACATCAACGGAAT
CTGGGGCATGTCTATGCATGTGCAGCGTTCTACCTTGGACCAAGTGAAGCAACACTTTGAAGTTAACAAGAAGAAGATGA
AAGAAAAGCAAAAGGACTATGGCTTTGAGGAGAGGATGAAGGAACTCAGAGAGGAGGAAGAGAAGGTCAAAGCATACAGG
AAGGGGAAGAAAAGAAAGGCAAAGGAAGACTTGACATTTGAGGAGGAGGATGAGATGTCAGCTGTTATGGGCTTCTTTGC
CTTTGGCTCCACCAAGAAGAGCTAC

Alignment

ORF - retro_mdom_1209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASGSGTKNLDFRRKWDKDEYEKLAEKRLNEERE-KKDGKPVQPVKRELLRHRDYKVDLESKLGKTIVIT
          .ASGS.TKNLDF.RKWDKDEYEK.AEKRL..ERE......PV.PVKRELLRHRDYK.DLESKLGKTIVIT
Retrocopy IASGSRTKNLDFCRKWDKDEYEKVAEKRLD*ERE<ENYRTPVKPVKRELLRHRDYKGDLESKLGKTIVIT

Parental  KTTPQSEMGGYYCNVCDCVVKDSINFLDHINGKKHQRNL-GMSMRVERSTLDQVKKRFEVNKKKMEEKQK
          KTTPQ....GYYCN.CD.VVKD.INFLDHINGKKHQRNL.GMSM.V.RSTLDQVK..FEVNKKKM.EKQK
Retrocopy KTTPQFQIRGYYCNICDSVVKDCINFLDHINGKKHQRNL>GMSMHVQRSTLDQVKQHFEVNKKKMKEKQK

Parental  DYDFEERMKELREEEEKAKAYKKEKQKEKKRRAEEDLTFEEDDEMAAVMGFSGFGSTKKSY
          DY.FEERMKELREEEEK.KAY.K.K....KR.A.EDLTFEE.DEM.AVMGF..FGSTKKSY
Retrocopy DYGFEERMKELREEEEKVKAYRKGK----KRKAKEDLTFEEEDEMSAVMGFFAFGSTKKSY

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	95.60 RPM
SRP007412_cerebellum	0.00 RPM	95.00 RPM
SRP007412_heart	0.00 RPM	41.86 RPM
SRP007412_kidney	0.00 RPM	46.09 RPM
SRP007412_liver	0.00 RPM	41.79 RPM
SRP007412_testis	0.00 RPM	88.20 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1209 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1209 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005907	1 retrocopy	retro_cfam_822,
Choloepus hoffmanni	ENSCHOG00000007795	2 retrocopies	retro_chof_101, retro_chof_514,
Callithrix jacchus	ENSCJAG00000016231	3 retrocopies	retro_cjac_1137, retro_cjac_1472, retro_cjac_4007,
Dipodomys ordii	ENSDORG00000014559	8 retrocopies	retro_dord_123, retro_dord_127, retro_dord_129, retro_dord_131, retro_dord_133, retro_dord_135, retro_dord_136, retro_dord_138,
Echinops telfairi	ENSETEG00000005406	2 retrocopies	retro_etel_156, retro_etel_882,
Ficedula albicollis	ENSFALG00000008988	1 retrocopy	retro_falb_9,
Myotis lucifugus	ENSMLUG00000017525	2 retrocopies	retro_mluc_2281, retro_mluc_2309,
Monodelphis domestica	ENSMODG00000011269	1 retrocopy	retro_mdom_1209 ,
Pteropus vampyrus	ENSPVAG00000009717	1 retrocopy	retro_pvam_827,
Ictidomys tridecemlineatus	ENSSTOG00000002025	1 retrocopy	retro_itri_1272,
Tursiops truncatus	ENSTTRG00000001777	4 retrocopies	retro_ttru_1889, retro_ttru_340, retro_ttru_721, retro_ttru_766,