RetrogeneDB ID: retro_mdom_1374

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:175508792..175509499(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000017505
• Aliases: None
• Description: None

Sequence

>retro_mdom_1374
ATGACCTCACGGGCTCCCAGCCTGGCTCCAGTGCCTCCACTGTGACTGGTGACTGACCTGCTCTTTGACATGGATGGCCT
CCTTCTGGATACTGAGCAACTCTATTCAGTGATATTCCAGGAAATCTGTGACTGCAATGGAAAGAAATATACATGGAGGT
GTGAAAGCTATGGTTATGGGTAAAAAGGCATTGGATGCAGCCCAGGTTATTGTAGAAGTCCTGGATCTTCCATTAACCAA
AGAGGAACTTTTGACAGAAAGCAAAAAGAAACAAGGAAAAGTATTTCCAACAACTATATTTATGCCAGGTATTGAGAAGC
TGATTAACCCGTCTACATAGATACAATATACCTATTGCTGTTGCTACTAGTTCAGTTGGATTGTCATTTGAGTGGAAGAC
AAGACACAAAGAATTCTTTAGTTTATTTAATCATCTTTTTTCTGAGCGATGACCCTGATATGAAGAGTGGCAAACCAGAG
CCGGACCTGTTTCTAACTTGTGCAAAGAGATTTCCCCTGCTCCTCCTGCTGAAAAGTGCCTTGTGTTTGAAGATGCTCCA
AATGGCTTTGAGGCAGCACTTGCAGATGGGATGCAGGTTATTATGGTTCCAGATGAACAATTAAACCCAGAGTTTACCAG
AAAGGTACCCTTAGTACTGAAATCACTGGAGGACTTTAAGATAGAGTTGTTTGGTTTGCCAACATGT

Alignment

ORF - retro_mdom_1374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.42 %
• Parental protein coverage: 93.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MASRAPGLAPAPPLRPVTHLLFDMDGLLLDTERLYSVIFQEICDCYGKKYTW-DVKAMVMGKKALDAAQV
          M.SRAP.LAP.PPL..VT.LLFDMDGLLLDTE.LYSVIFQEICDC.GKKYTW..VKAMVMGKKALDAAQV
Retrocopy MTSRAPSLAPVPPL*LVTDLLFDMDGLLLDTEQLYSVIFQEICDCNGKKYTW>GVKAMVMGKKALDAAQV

Parental  IVEVLDLPLTKEELLTESKKKQEQVFPTTTFMPGVEKLIN-HLHRHNIPIAVATSSAGLSFEWKTSRHKE
          IVEVLDLPLTKEELLTESKKKQ..VFPTT.FMPG.EKLIN..LHR.NIPIAVATSS.GLSFEWKT.RHKE
Retrocopy IVEVLDLPLTKEELLTESKKKQGKVFPTTIFMPGIEKLIN>RLHRYNIPIAVATSSVGLSFEWKT-RHKE

Parental  FFSLFNHLV-LGDDPDVKSGKPEPDLFLTCAKRF-SPAPPAEQCLVFEDAPNGVEAALAAGMQVVMVPDE
          FFSLFNHL..L.DDPD.KSGKPEPDLFLTCAKRF.SPAPPAE.CLVFEDAPNG.EAALA.GMQV.MVPDE
Retrocopy FFSLFNHLF>LSDDPDMKSGKPEPDLFLTCAKRF<SPAPPAEKCLVFEDAPNGFEAALADGMQVIMVPDE

Parental  QLNPEFTRKATLVLKSLEDFKPELFVAKNC
          QLNPEFTRK..LVLKSLEDFK.ELF....C
Retrocopy QLNPEFTRKVPLVLKSLEDFKIELFGLPTC

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_1374 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1374 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004616	1 retrocopy	retro_acar_48,
Choloepus hoffmanni	ENSCHOG00000001318	5 retrocopies	retro_chof_1597, retro_chof_1855, retro_chof_1883, retro_chof_2136, retro_chof_2168,
Homo sapiens	ENSG00000130021	2 retrocopies	retro_hsap_2469, retro_hsap_454,
Gorilla gorilla	ENSGGOG00000004425	1 retrocopy	retro_ggor_1537,
Microcebus murinus	ENSMICG00000017082	1 retrocopy	retro_mmur_1321,
Macaca mulatta	ENSMMUG00000017377	1 retrocopy	retro_mmul_244,
Monodelphis domestica	ENSMODG00000017505	2 retrocopies	retro_mdom_1374 , retro_mdom_52,
Pongo abelii	ENSPPYG00000020105	2 retrocopies	retro_pabe_1837, retro_pabe_280,
Pteropus vampyrus	ENSPVAG00000011149	1 retrocopy	retro_pvam_1165,
Tarsius syrichta	ENSTSYG00000013238	4 retrocopies	retro_tsyr_2013, retro_tsyr_345, retro_tsyr_542, retro_tsyr_931,