RetrogeneDB ID: retro_oana_44

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Contig19872:7365..7749(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ox_plat1_531208
• Ensembl ID: ENSOANG00000020728
• Aliases: None
• Description: None

Sequence

>retro_oana_44
CCCGAAGTCATGGAGTAATACTAGGTCAAGGGATGTGAATTAATTGAGACTGCTGATCAAAACTTCACTGACTTCACTAA
GTGTTTAAAAGTGCCCCTAGAAAAGATAAAAGGAAAGGACCTGCAGGTTGATATGATTGTGACACTGAGCAGACTTGGAG
GACGTTTTGACCAGCTTATGGCTTCCGTGGAAACCCTCTTTCATGCGACCAACCTCACCTCTTTGCCTATTGTAGTGATC
CAAGAAGATTCCTTCATCTACCTCCTTCAGCCAGGGAAGCACAGACTGCAGGTTAACACCGGATTGGAAGGGGAATAGTG
TGGCCTCATTCCAGTTGGATTTCCTTGCCACGTCACTACCACAGGACTGAAGTGGAACCTCACT

Alignment

ORF - retro_oana_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.62 %
• Parental protein coverage: 55.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PEVMEYYKVKGCELIETADQNFTDFTKCLKVLLEKIKEKDLQVDMIVTLGGLGGRFDQIMASVETLFHAT
          PEVME.Y.VKGCELIETADQNFTDFTKCLKV.LEKIK.KDLQVDMIVTL..LGGRFDQ.MASVETLFHAT
Retrocopy PEVME*Y*VKGCELIETADQNFTDFTKCLKVPLEKIKGKDLQVDMIVTLSRLGGRFDQLMASVETLFHAT

Parental  SLTSLPIVVIQEDSLVYLLQPGKHRLQVNTGLEGEWCGLIPVGFPCRVTTTGLKWNLT
          .LTSLPIVVIQEDS..YLLQPGKHRLQVNTGLEGE.CGLIPVGFPC.VTTTGLKWNLT
Retrocopy NLTSLPIVVIQEDSFIYLLQPGKHRLQVNTGLEGE*CGLIPVGFPCHVTTTGLKWNLT

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	1.77 RPM
SRP007412_cerebellum	0.00 RPM	1.40 RPM
SRP007412_heart	0.00 RPM	1.86 RPM
SRP007412_kidney	0.00 RPM	7.40 RPM
SRP007412_liver	0.00 RPM	4.07 RPM
SRP007412_testis	0.00 RPM	4.15 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_44 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_44 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus 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.

---

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,