RetrogeneDB ID: retro_mdom_1270

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:201335027..201335816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005918
• Aliases: None
• Description: None

Sequence

>retro_mdom_1270
ATGTCATCTTTCCCCGAACTCTACTTCAACATGGACAATGGCTACTTGAAGGGCTTGGTCTGGGGCTTCAAGGCCGGGGT
GCTGAGCCAGCAGGATTGCCTCAACCTGGTGCAGTGCAAGACTCTTGAGGATCTGAAATTACACCTCCAGAGCACAGACT
ATGGGAACTTCCTGGCGAATGAGGTATCCCCACTCACTGTGTCTGTCATTGACAACAAACTCAAGGAGAAGATGGTGATG
GAGTTCCGTCACATGAGGAATCATGCCCATGAACCACTGGCCAGCTTCCTGGACTTCATCACCTACAGCTACATGATTGA
TAATGTCATCCTGCTGATAACAGGGACCTTGCACCAGCGCTCCATTGTTGAGCTTGTGCCCAAGTGCCACCCACTAGGCA
GCTTTGAGCAGATGGAGGCCTGGAACATTGCTCAGACTCCAGCCGAATTATATAATGCTATCTTAGTGGACACCCCACTC
GGTGCATTCTTCTAAGACTGCATCTCTGAGCAGGACCTCGGCGAGATGAACATCGAAATCATCTGTAACACACTGTACAA
GGCCTACCTAGAGTCCTTCTACAAGTTCTGCACCTTGCCGGGGGGCACCACAGCAGACGCCACGCGTCCTATCCTGGAGT
TTGAGGCCAACCGCAGGGCCTTCATCATCACCATCAACTCCTTTGGCACTGAGTTCTCCAAGGAGGACTGGGCCAAGCTG
TTCCCACATTGTGGGAAGCTCTACCCTGAGGGCCTGGCCCAGCTGGCCCCGGCTGATGACTACGAGCAG

Alignment

ORF - retro_mdom_1270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.02 %
• Parental protein coverage: 74.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSFPELYFNVDNGYLEGLVRGFKAGVLSQQDYLNLVQCETLEDLKLHLQSTDYGNFLANEASPLTVSVI
          MSSFPELYFN.DNGYL.GLV.GFKAGVLSQQD.LNLVQC.TLEDLKLHLQSTDYGNFLANE.SPLTVSVI
Retrocopy MSSFPELYFNMDNGYLKGLVWGFKAGVLSQQDCLNLVQCKTLEDLKLHLQSTDYGNFLANEVSPLTVSVI

Parental  DDKLKEKMVMEFRHMRNHAYEPLASFLDFITYSYMIDNVILLITGTLHQRSIAELVPKCHPLGSFEQMEA
          D.KLKEKMVMEFRHMRNHA.EPLASFLDFITYSYMIDNVILLITGTLHQRSI.ELVPKCHPLGSFEQMEA
Retrocopy DNKLKEKMVMEFRHMRNHAHEPLASFLDFITYSYMIDNVILLITGTLHQRSIVELVPKCHPLGSFEQMEA

Parental  VNIAQTPAELYNAILVDTPLAAFFQDCISEQDLDEMNIEIIRNTLYKAYLESFYKFCTLLGGTTADAMCP
          .NIAQTPAELYNAILVDTPL.AFF.DCISEQDL.EMNIEII.NTLYKAYLESFYKFCTL.GGTTADA..P
Retrocopy WNIAQTPAELYNAILVDTPLGAFF*DCISEQDLGEMNIEIICNTLYKAYLESFYKFCTLPGGTTADATRP

Parental  ILEFEADRRAFIITINSFGTELSKEDRAKLFPHCGKLYPEGLAQLARADDYEQ
          ILEFEA.RRAFIITINSFGTE.SKED.AKLFPHCGKLYPEGLAQLA.ADDYEQ
Retrocopy ILEFEANRRAFIITINSFGTEFSKEDWAKLFPHCGKLYPEGLAQLAPADDYEQ

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_1270 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1270 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014351	1 retrocopy	retro_meug_1680,
Monodelphis domestica	ENSMODG00000005918	2 retrocopies	retro_mdom_1270 , retro_mdom_259,
Sarcophilus harrisii	ENSSHAG00000013154	1 retrocopy	retro_shar_102,