RetrogeneDB ID: retro_mdom_752

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:331149601..331150227(+)
• Located in intron of: ENSMODG00000018477

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_752
AGAAAGCTTGCTTTGAAGCTTCATTCAGATAAAAACCATGCACCTGGAGCAATAGATGCTTTTAAAAAGATAAGAAATGC
CTATGCAGTTTTAAGCAATCCTGAAAAAAAGAAAGCAGTATGACCTCACAGGCAATGAAGACCAAGCGTGTAGTCACCAA
AACAATGGTAGATTTAATTTCCATAGAGGCTGTGAAGCTGATATAACTCCAGAAGATTGTTTAATATATTCTTTGGTGGT
GGATTTCCATCAAGTAGTGTACATTCATTTTCTAATGGAAGAGCTGTATATAGACATTACCACCAACACCGGCATAGTGG
ACATTGAGAGAGAAGAAGAAAGAGGTGCTGGAGGGTTCTCTGTGTTTATACAGCTGATGCCCATTGTAGTTTTGATTCTT
GTGTCTTTGTTAAGTCAGTTGATGGTCTCTAATCCTAATTACTCCTTATATCCCAGATCTGGTTCAGGACAAACTTTTAA
AATGCAGACAGAAAACTTTGGGTGTCATTTATTATGTCAACAAGGAGTTTAAGAATGACTACAAAGGAACGTTATTACAA
AGGGTAGAAAGAAGTATGGAAGAAAATTATGTAACTAATATTTGAAATAATTGCTGGAAAGAAAGA

Alignment

ORF - retro_mdom_752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.09 %
• Parental protein coverage: 55.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKLALKFHPDKNHAPGATDAFKKIGNAYAVLSNPEK-RKQYDLTGNEDQACNHQNNGRFNFHRGCEADIT
          RKLALK.H.DKNHAPGA.DAFKKI.NAYAVLSNPEK.RKQYDLTGNEDQAC.HQNNGRFNFHRGCEADIT
Retrocopy RKLALKLHSDKNHAPGAIDAFKKIRNAYAVLSNPEK>RKQYDLTGNEDQACSHQNNGRFNFHRGCEADIT

Parental  PED-LFNIFFGGGFPSGSVHSFSNGRAGYSHHHQHRHSGH-EREEERGDGGFSVFIQLMPIVVLILVSLL
          PED.LFNIFFGGGFPS.SVHSFSNGRA.Y.H.HQHRHSGH.EREEERG.GGFSVFIQLMPIVVLILVSLL
Retrocopy PED<LFNIFFGGGFPSSSVHSFSNGRAVYRHYHQHRHSGH>EREEERGAGGFSVFIQLMPIVVLILVSLL

Parental  SQLMVSNPPYSLYPRSGSGQTFKMQTEN-LGVVYYVNKEFKNDYKGTLLQKVEKSVEEDYVTNIRNNCWK
          SQLMVSNP.YSLYPRSGSGQTFKMQTEN.LGV.YYVNKEFKNDYKGTLLQ.VE.S.EE.YVTNI.NNCWK
Retrocopy SQLMVSNPNYSLYPRSGSGQTFKMQTEN>LGVIYYVNKEFKNDYKGTLLQRVERSMEENYVTNI*NNCWK

Parental  ER
          ER
Retrocopy ER

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_752 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_752 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,