RetrogeneDB ID: retro_mdom_1398

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:279071144..279071990(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020687
• Aliases: None
• Description: None

Sequence

>retro_mdom_1398
ATGGAGGGGAACCAGGACGAGGCAGAGAAATGCATTGAGATCAGCAGGGAAGCTCTGGAGGCTGACAATTGTGACTGGGC
CCTGTACTTCCTGCACAAGGTAGAGAAGCTCTATCCATCCCCTTCGGCCCAAGTACTTCTGGAAGCAATTATGAAAAATG
GAAGCACAACTGCAAATGGACCACATGGCCGAAAACTGTGAAGTGGTGGTGATCATAACAGACCCAATAATACAAAGGAC
AGAGCTGGTGGTGAAAGTGGAAAATCCTATACCAAAGCTCAAGTAGATGGAGTCCTCAGCATAAACAAAGTGTAAAATTA
CTATGAAGTACTGGGAATCACAAAAGATGCCAGTGATGAGGATTTGAAGAAAGCTTACAGAAAGCTTGCTTTGAAGTTTC
ATCCAGATAAAAACCATGCACCTGGAGCAACAGATGCTTTTAAGATTGGAAATGCCTATGCAGTTTTAAGCAATCCTGAA
AAAAGAAAGCAATATGACTTTACAGGCAATGAAAACCAAGTATGTAATCACCAAAATAATGGTAGATTTAATTTCCACAG
AGGCTGTGAAACTGATATAACACCAGAATATTTGTTTGATATGTTCTTTGGTGGTGGATTTCCATCAGGTAGTGTACATA
CATTTTCTAATGGAAGAGCTTGTTATAGCCATCACCACCAACACAGGCATAGTGGACATGAGAGAGAAGAAAGAGGCGAT
GGAGGGTTGTCTGTGTTTATACAGCTAATGCCCATTATAGTCTTGGTTCTTGTGTTCTTGTTAAGCCAGTTGATGGTCTC
TAATCCTCCTTATTCCCTATATTCCAAAACTGGTTCAGGATAAACT

Alignment

ORF - retro_mdom_1398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 75.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGNRDEAEKCIEIAREALEAGNRDRALRFLHKAEKLYPSPTARVLLEAIMKNGSTAANGPHCRKPSSGG
          MEGN.DEAEKCIEI.REALEA.N.D.AL.FLHK.EKLYPSP.A.VLLEAIMKNGST.ANGPH.RK..SGG
Retrocopy MEGNQDEAEKCIEISREALEADNCDWALYFLHKVEKLYPSPSAQVLLEAIMKNGSTTANGPHGRKL*SGG

Parental  DHNRPNNTKDSAGGESGKAYTKDQVDGVLSINKCKNYYEVLGVTKDASDEDLKKAYRKLALKFHPDKNHA
          DHNRPNNTKD.AGGESGK.YTK.QVDGVLSINK..NYYEVLG.TKDASDEDLKKAYRKLALKFHPDKNHA
Retrocopy DHNRPNNTKDRAGGESGKSYTKAQVDGVLSINKV*NYYEVLGITKDASDEDLKKAYRKLALKFHPDKNHA

Parental  PGATDAFKKIGNAYAVLSNPEKRKQYDLTGNEDQACNHQNNGRFNFHRGCEADITPEDLFNIFFGGGFPS
          PGATDAFK.IGNAYAVLSNPEKRKQYD.TGNE.Q.CNHQNNGRFNFHRGCE.DITPE.LF..FFGGGFPS
Retrocopy PGATDAFK-IGNAYAVLSNPEKRKQYDFTGNENQVCNHQNNGRFNFHRGCETDITPEYLFDMFFGGGFPS

Parental  GSVHSFSNGRAGYSHHHQHRHSGHEREEERGDGGFSVFIQLMPIVVLILVSLLSQLMVSNPPYSLYPRSG
          GSVH.FSNGRA.YSHHHQHRHSGHER.EERGDGG.SVFIQLMPI.VL.LV.LLSQLMVSNPPYSLY...G
Retrocopy GSVHTFSNGRACYSHHHQHRHSGHER-EERGDGGLSVFIQLMPIIVLVLVFLLSQLMVSNPPYSLYSKTG

Parental  SGQT
          SG.T
Retrocopy SG*T

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_1398 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1398 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012468	1 retrocopy	retro_acar_144,
Homo sapiens	ENSG00000164031	1 retrocopy	retro_hsap_1583,
Monodelphis domestica	ENSMODG00000020687	2 retrocopies	retro_mdom_1398 , retro_mdom_752,
Nomascus leucogenys	ENSNLEG00000013668	2 retrocopies	retro_nleu_1761, retro_nleu_2409,
Otolemur garnettii	ENSOGAG00000005340	1 retrocopy	retro_ogar_120,
Pongo abelii	ENSPPYG00000014956	3 retrocopies	retro_pabe_1304, retro_pabe_982, retro_pabe_983,
Pan troglodytes	ENSPTRG00000016311	1 retrocopy	retro_ptro_1066,
Ictidomys tridecemlineatus	ENSSTOG00000021338	1 retrocopy	retro_itri_1840,