RetrogeneDB ID: retro_mdom_1439

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:70259030..70259985(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013650
• Aliases: None
• Description: None

Sequence

>retro_mdom_1439
ACTCTGGATTCAGAGATATGCCACACAAGCCTGTTCTACCGCCCAAGCCCAGATGGAAATTTGACCATCTTAAGGACTAA
TCAGGCAGAAGTTCCTATTGGGTGTCACTATCCTAGGTGGGGCAATGTAAGTAGCAGAGCTATCCAGCCTACATGGGTCC
CCTTCAGGACCACCATAGCCTCTGAAGAGAAGCTCAGCTTCTCTCTTTGTCTGATGAATGATAACTGGACTTCTGAGAGT
ACCTCAGCTGAGTTCCAGCTGGGTGACATAGCCCATCTCTAGGCAAAAGTCCACACAGGCAGCCATGTGTCCCTGAGGCT
CTTTGATGACATCTGTGTGGCCACCCTTAGCCCAGACAAGGACTCAGAGCCCCGTTACAGTATCATTGACCACCATGGGT
GCCTGGTAGATGGTCTTTCTGACTCCTCTTCAGTCTTCAGAATCCCCAGACCTAACCCAAACACTCTCCAGTTCACAGTG
GACTTGTTCCACTTTGACAGTGATCCTCAGAAACTGATTTATATTATGTATCATCTGATGGTCACTCTCATTGACCAAGA
GCCAGACCAAACAAACAAGGCCTGTTCTTTCAACAAGTCCACTAGTAGCTGGTTTCCAGTAGAAGGCCCTTCTGACATCT
GCAGATGCTGTAATATCAAAGACTGCGGAATTCCAAACCAGTCCAGGAGACTACTTTCTGTTGACAGGATCTCTGCAAAG
CCCTGGAAGAGAACAGCTCCCCTCCAGCAGCTGCAAGTGAGGGAAGCTGATGTCACTGCCGGGGCCCATGTTCTTGGCAG
TGAATGTCAATCACCACACCCCACTGGAGCCCAACCCGGATTTCATGGAAAAGAACACAGCCTTTGGCCTGAGCCTGTCT
CTGATTGATCTTGTGTTTCTTGCCATAGTCATGCTGGCCCTGGTCCTCCTCTGTAGTAAACACAAAAGTGCCTCT

Alignment

ORF - retro_mdom_1439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.03 %
• Parental protein coverage: 76.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSDELIYRTSLFYRPSPDGNLTILRTNQAEVPIECHYPRWGNVSSRAIQPTWVPFRSTIASEEKLSFSLR
          T.D..I..TSLFYRPSPDGNLTILRTNQAEVPI.CHYPRWGNVSSRAIQPTWVPFR.TIASEEKLSFSL.
Retrocopy TLDSEICHTSLFYRPSPDGNLTILRTNQAEVPIGCHYPRWGNVSSRAIQPTWVPFRTTIASEEKLSFSLC

Parental  LMNDNWTSESTSAEFQLGDIAHLQAEVHTGSHVSLRLFVDSCVATLSPDKDSEPRYSIIDHHGCLVDGLS
          LMNDNWTSESTSAEFQLGDIAHL.A.VHTGSHVSLRLF.D.CVATLSPDKDSEPRYSIIDHHGCLVDGLS
Retrocopy LMNDNWTSESTSAEFQLGDIAHL*AKVHTGSHVSLRLFDDICVATLSPDKDSEPRYSIIDHHGCLVDGLS

Parental  DSSSVFRTPRPNPNTLQFTVDLFHFVSDPRKLIYITCHLTVTLTDQEPDQTNKACSFNKSTNSWFPVEGP
          DSSSVFR.PRPNPNTLQFTVDLFHF.SDP.KLIYI..HL.VTL.DQEPDQTNKACSFNKST.SWFPVEGP
Retrocopy DSSSVFRIPRPNPNTLQFTVDLFHFDSDPQKLIYIMYHLMVTLIDQEPDQTNKACSFNKSTSSWFPVEGP

Parental  PDICRCCNTKDCRIPNRSRRRLSVDRISAKPWKRTAPLQQLQVREADVTA-GPMFLAVNFSRHTPLEPNP
          .DICRCCN.KDC.IPN.SRR.LSVDRISAKPWKRTAPLQQLQVREADVTA.GPMFLAVN...HTPLEPNP
Retrocopy SDICRCCNIKDCGIPNQSRRLLSVDRISAKPWKRTAPLQQLQVREADVTA>GPMFLAVNVNHHTPLEPNP

Parental  DFMEKYTAFGLSLSLIALVVLAIVMLALVLLCRKRNSAS
          DFMEK.TAFGLSLSLI.LV.LAIVMLALVLLC.K..SAS
Retrocopy DFMEKNTAFGLSLSLIDLVFLAIVMLALVLLCSKHKSAS

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_1439 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1439 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013031	1 retrocopy	retro_eeur_494,
Monodelphis domestica	ENSMODG00000013650	1 retrocopy	retro_mdom_1439 ,
Sarcophilus harrisii	ENSSHAG00000016866	1 retrocopy	retro_shar_385,