RetrogeneDB ID: retro_mdom_1299

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:349312412..349313156(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024002
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025468
• Aliases: None
• Description: None

Sequence

>retro_mdom_1299
ATGGAGCATATCCTTTCCCCACTGGAATGCCTGCTTCCCACTGGAGATCTGAAGTATTGCCTCTTGATCCTGAATCAGCC
TTTGGACAGAAGACCACTTCATCATCTATGGAGCAAAGCTCTTCTAAGAGCATGTGCTGATGGAGGTTCCAACCACTTGT
ATGATATCACTGAAGGCCAGCGGGAGAGCTTCTTACCCGAGTACATCAGTGGAGATTTTGATTCTATTAGGCCTGAAGTC
AAAGAGTATTACCAAGTCAAGGGATGTGAGCTTGTTAAAACCCCTGATCAAAATTACACCGATTTTACGAAATGCCTTCA
AGTCCTACAGAAGAAGATAGTAGACAAAGATCTCCAGGTGGACATGATTGTGGCACTGGGTGGCCTGGCAGGACGTTTTG
ACCAGATCATGGCTTCTGTAGAGACCCTTTTTCATGCAACTGCCATCACTCCAGTGCCTGTTATCATCATACAAGCAGAT
TCCCTCATTTGCCTGCTTCAGCCGGGAAAGCACCAACTGCATGTAGACACGGGTTTGGAAGGGGATTGGTGTGGCCTTGT
TCCTGTTGGACAGCCCTGTAAGCAAGTCACCACAACAGGCCTCAAATGGAACCTCACCAAGGATGTCCTCATGTTTGGAA
CGCTAGTCAGCACTTCCAATACCTATGATGGCTCTGGAGTTGTGACCGTGGAAACAGATCATCCACTCCTCTGGACCATG
GGTATCAAAGGTGATCCCAGAGAA

Alignment

ORF - retro_mdom_1299 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEHILSPLECLLPTGNLKYCLLILNQPLDRSQFHHLWSKALLKACADGGSNRLYDITEGQRESFLPEYIS
          MEHILSPLECLLPTG.LKYCLLILNQPLDR...HHLWSKALL.ACADGGSN.LYDITEGQRESFLPEYIS
Retrocopy MEHILSPLECLLPTGDLKYCLLILNQPLDRRPLHHLWSKALLRACADGGSNHLYDITEGQRESFLPEYIS

Parental  GDFDSIRPEVKEYYKVKGCELVSTPDQNYTDFTKCLQVLQKKIVEKDLQVDMIVTLGGLAGRFDQIMASV
          GDFDSIRPEVKEYY.VKGCELV.TPDQNYTDFTKCLQVLQKKIV.KDLQVDMIV.LGGLAGRFDQIMASV
Retrocopy GDFDSIRPEVKEYYQVKGCELVKTPDQNYTDFTKCLQVLQKKIVDKDLQVDMIVALGGLAGRFDQIMASV

Parental  ETLFHATSITPVPIIIIQADSLICLLQQGKHKLHVDTGLEGNWCGLVPVGHPCKHVTTTGLKWNLTNDVL
          ETLFHAT.ITPVP.IIIQADSLICLLQ.GKH.LHVDTGLEG.WCGLVPVG.PCK.VTTTGLKWNLT.DVL
Retrocopy ETLFHATAITPVPVIIIQADSLICLLQPGKHQLHVDTGLEGDWCGLVPVGQPCKQVTTTGLKWNLTKDVL

Parental  MFGTLVSTSNTYDGSGVVTVETDHPLIWTMGIKNEPRE
          MFGTLVSTSNTYDGSGVVTVETDHPL.WTMGIK..PRE
Retrocopy MFGTLVSTSNTYDGSGVVTVETDHPLLWTMGIKGDPRE

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_1299 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1299 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 7 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001227	23 retrocopies	retro_chof_1004, retro_chof_1093, retro_chof_1416, retro_chof_1458, retro_chof_1537, retro_chof_1683, retro_chof_1732, retro_chof_191, retro_chof_1927, retro_chof_2202, retro_chof_2413, retro_chof_2507, retro_chof_2577, retro_chof_468, retro_chof_472, retro_chof_550, retro_chof_630, retro_chof_665, retro_chof_701, retro_chof_801, retro_chof_917, retro_chof_954, retro_chof_988,
Dasypus novemcinctus	ENSDNOG00000018545	4 retrocopies	retro_dnov_1080, retro_dnov_1592, retro_dnov_2405, retro_dnov_2523,
Macropus eugenii	ENSMEUG00000010062	1 retrocopy	retro_meug_1153,
Myotis lucifugus	ENSMLUG00000004213	1 retrocopy	retro_mluc_1071,
Monodelphis domestica	ENSMODG00000025468	2 retrocopies	retro_mdom_1299 , retro_mdom_1300,
Ornithorhynchus anatinus	ENSOANG00000020728	1 retrocopy	retro_oana_44,
Vicugna pacos	ENSVPAG00000010214	2 retrocopies	retro_vpac_205, retro_vpac_503,