RetrogeneDB ID: retro_mdom_24

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:177754477..177755200(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024803
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008300
• Aliases: None
• Description: None

Sequence

>retro_mdom_24
ATGAGTCTCCAGTGGGCAGCGGTGGCCACCTTCTTCTATGCGGAGATCCTGGCAGCAGTGCTTCTCTGCAGCCCCTTCAT
CTCCCCACAGAAATGGCTGAAGATCTTCAGATCTCGCCTGGTACGCCAGGTGGTGAACCGTGGGAAGCCCTACTTCTCAG
TTCTCCTGCTAATCCTGGTGCTGCTCTTTATGGATGCCCTCTGGGAGATGAGAAAGTTTGACTCCTCCGAGAAGAAGGGC
CTGCGGAACAATACCGTGGCTTTGGAGCAATATCACATGAAGCTCTACCGAGCCCAGTGGAACCTGCACCTCACCAGCTT
CTCGCTCCTGATGTCGCTGCTGCTCCGCCGCCTGGTCACCCTCCAGAGCCAACAGGCCTTGCTGCAGGCCTCCCGAGAGG
CCTTACGGAGGCAGGCGCTGGGGGCCCTTGAGGCGGCGCAGCGGTTCCTCGACGAGAATGAGAGGCTGAGAGCAGAGGTC
GGGAGCGATAGTGCTGCCCAGCTGAGTGCTGCCCCGGTGAGCGATGAAAACCAGTGCTTGAGGGAGGAGCTCAAGAAGCT
GACAGAAGAGCTGGAAAACAGCCGCAGGAACCTGGAGTCCGCTCAGGACGAGGCCCTGGCCCTGCGCAAGCGCTGTGAGG
GGGTCCCCCAAGAGCATGACCACTTGGCTGAGCAGCACCATGAGGCGGGGGAGGGGCTCCCTGAAGACCAGAAAAACAAG
TGA

Alignment

ORF - retro_mdom_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.07 %
• Parental protein coverage: 93.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLQWTAVATFLYAEVFAVLLLCIPFISPKRWQKIFKSRLVQLVVSYGNTFFVVLIVILVLLLIDAVREI
          MSLQW.AVATF.YAE..A..LLC.PFISP..W.KIF.SRLV..VV..G...F.VL..ILVLL..DA..E.
Retrocopy MSLQWAAVATFFYAEILAAVLLCSPFISPQKWLKIFRSRLVRQVVNRGKPYFSVLLLILVLLFMDALWEM

Parental  RKYDDVTEKVNLQNNPGAMEHFHMKLFRAQRNLHIAGFSLLLSFLLRRLVTLISQQATLLASNEAFKKQA
          RK.D...EK..L.NN..A.E..HMKL.RAQ.NLH...FSLL.S.LLRRLVTL.SQQA.L.AS.EA...QA
Retrocopy RKFDS-SEKKGLRNNTVALEQYHMKLYRAQWNLHLTSFSLLMSLLLRRLVTLQSQQALLQASREALRRQA

Parental  EGASEAAKKYIEENDKLKKGAGTGVGKLDLKDEVLAENKNLKAELKKLTQELAVNKRSLEKAENEALAMR
          .GA.EAA.....EN..L....G...........V..EN..L..ELKKLT.EL....R.LE.A..EALA.R
Retrocopy LGALEAAQRFLDENERLRAEVGSDSAAQLSAAPVSDENQCLREELKKLTEELENSRRNLESAQDEALALR

Parental  KQSDGLTKEYDRLLEEH
          K...G...E.D.L.E.H
Retrocopy KRCEGVPQEHDHLAEQH

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_24 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_24 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019245	1 retrocopy	retro_cfam_482,
Callithrix jacchus	ENSCJAG00000011348	1 retrocopy	retro_cjac_2552,
Echinops telfairi	ENSETEG00000008662	1 retrocopy	retro_etel_1522,
Macropus eugenii	ENSMEUG00000007345	3 retrocopies	retro_meug_1017, retro_meug_1867, retro_meug_208,
Monodelphis domestica	ENSMODG00000008300	2 retrocopies	retro_mdom_1110, retro_mdom_24 ,
Sarcophilus harrisii	ENSSHAG00000009111	1 retrocopy	retro_shar_31,