RetrogeneDB ID: retro_mdom_278

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:11987345..11988176(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025396
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021047
• Aliases: None
• Description: None

Sequence

>retro_mdom_278
ATGTCCTCCAGCAGCCGAGTAGCCGTGGTGACAGGAAGTAACAAGGGCATCGGCTTCGCCATCGTGCGCAATCTGTGCCA
GAAGTCCTCGGGAGATGTGATTCTCACGTCCCGGGACACGACGCGGGGCCAGGCGGCTACGAAGAAGCTGCAGGAAGAGG
GACTCAACCTGATTTTCCACCAGCTGGACATCGATGACCCACAGAGCATCCGGACCCTGCGGGATTTTCTCAAGGAGTGC
TACGGGGGTGTGGACGTGCTGGTCAACAATGTGGGAATCGCCTTCAAAGTCGCTGATACCACACCTTTTCCTATTCAAGC
TGAAGTGACCATGAAAACCAACTTTTTTGGCACCAAAGCTGTATCTGCAGAATTACTGCCTTTAGTAAAACCCCGAGGCA
GAGTGGTGAATGTCTCTAGCATGGTGAGCTTACGTTCTCTTAAAAGCTGCAGCCCAGAACTACAGCAGAAGTTTCGCAGT
GACACAATCACAGAGGAAGAGCTGGTGAGGCTCATGGAAAAATTTGTGGAGGATACAAAGAAAGGAGTGCATCAGAAGGA
AGGTTGGCCCAACAGTGCTTATGGAGTGACCAAGATTGGAGTCACTGTGTTGTCTATCCATGCCAGGCAGCTGAATGAGC
AAAGGAAAGGTGATAAGATTCTTCTGAATGCCTGCTGCCCAGGATGGGTGAGAACTGACATGGCAGGGCCCAAGGCTACC
AAGAGTCCAGAAGAAGGAGCTGAAACCCCAGTTTATTTGGCTCTTTTGCCCCCAGATGCTACAGAACCTCACGGCCAATT
TGTCATGGAGAAAAGGGTTGAAAAATGGTAA

Alignment

ORF - retro_mdom_278 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 72.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFLKERYGGVDVLVNNAGIAFKAEVTMKTNFFGIKAVSAELLPLVKPGGRVVNISSMMSLRALEGCSPEL
          D.L....G..............AEVTMKTNFFG.KAVSAELLPLVKP.GRVVN.SSM.SLR.L..CSPEL
Retrocopy DVLVNNVGIAFKVADTTPFPIQAEVTMKTNFFGTKAVSAELLPLVKPRGRVVNVSSMVSLRSLKSCSPEL

Parental  QQKFRSDTITEEELVRLMEKFVEDTKKGVHQKEGWPNSAYGVTKIGVTVLSRIHARQLNEQRKGDKILLN
          QQKFRSDTITEEELVRLMEKFVEDTKKGVHQKEGWPNSAYGVTKIGVTVLS.IHARQLNEQRKGDKILLN
Retrocopy QQKFRSDTITEEELVRLMEKFVEDTKKGVHQKEGWPNSAYGVTKIGVTVLS-IHARQLNEQRKGDKILLN

Parental  ACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDATEPHGQFVMEKRVEKW
          ACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDATEPHGQFVMEKRVEKW
Retrocopy ACCPGWVRTDMAGPKATKSPEEGAETPVYLALLPPDATEPHGQFVMEKRVEKW

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_278 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_278 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031486	1 retrocopy	retro_cfam_1498,
Callithrix jacchus	ENSCJAG00000038083	1 retrocopy	retro_cjac_1139,
Echinops telfairi	ENSETEG00000005109	1 retrocopy	retro_etel_433,
Felis catus	ENSFCAG00000025135	1 retrocopy	retro_fcat_118,
Monodelphis domestica	ENSMODG00000021047	1 retrocopy	retro_mdom_278 ,