RetrogeneDB ID: retro_fcat_1125

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:137052206..137052988(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDAP2
• Ensembl ID: ENSFCAG00000003468
• Aliases: None
• Description: ganglioside induced differentiation associated protein 2 [Source:HGNC Symbol;Acc:18010]

Sequence

>retro_fcat_1125
ATAGATTCCATAGGGGCACAATCCCAGTTTGTGGATGTAGATAGGTACAGAGAGCTAGGCAACTGTGTGAAGATGAATTA
AATGCTTCTAATACTGCAGCTGAAACATTTTGGAAAGACGCTATTAAATCACCTTTTATTTTTTATAATAAGGATATCAA
TGAAAAAAGTGGTCCTCTGGAAAGGAGACGTGGCATTACTGATCAACATACCACCCTTGTGAATACCAGCAACGAATGTC
TCACAAAGAAAAATCCTGTGTCAGAAAGTATCTTCATGCTTGTGGGGCCTGATCTGAAGGAGGAATTCCAGAAACTTAAA
GGTTGATTAACAGGTAAAGAGAAATTGACAAAAGGATTTAAGATCGCCACCATTTAATCAATCACACATCAGAACCTAAA
TATAAGAGCCACTATCCAACAGCACCTGAGGGTTCCCTATAAGGCTGCTAAAGACGCATAGTTCAGAAAAAGAGTAGTCA
GTGTCTTCGTTTGCATTCTGTGTCATCTGTTTCTGCAAAACAAATTTATCCTTAGAGAATGAAACATACACAGCACTTTG
CATTGTAAGGAAATTCCTAGAGATATATGAAGAGACCACAAAAAAGTAAGATTTGCTGTCTCTAAACTAAAAGTGGCTAC
TTATCAAGAGCTGCCACTTCCAGAGTTCTCAAGGTCATTAAAAGAGAGTCGATCACAGCCATACCTACCTGAGGATGTTG
AGAATGTAGAAAGATGGACTGTGGGACCTAAAGGGAAGATTAGAATAAGTGAAAAACTTGGT

Alignment

ORF - retro_fcat_1125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.04 %
• Parental protein coverage: 52.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MDPLGAPSQFVDVDTLPSWGDS-CEDELNTSDTAAETLQENTVRSPFL-YNKDISGK-VILWKGDVA-LL
          .D..GA.SQFVDVD.....G...CEDELN.S.TAAET.......SPF..YNKDI..K.V.LWKGDVA.L.
Retrocopy IDSIGAQSQFVDVDRYRELGNC<CEDELNASNTAAETFWKDAIKSPFIFYNKDINEK>VVLWKGDVALLI

Parental  NC-TAIVNTSNESLTDKNPVSESIFMLAGPDLKEDLQKLKGCRTGEAKLTKGFNLAA-RFIIHTVGPKYK
          N..T..VNTSNE.LT.KNPVSESIFML.GPDLKE..QKLKG..TG..KLTKGF..A....I.HT..PKYK
Retrocopy NI<TTLVNTSNECLTKKNPVSESIFMLVGPDLKEEFQKLKG*LTGKEKLTKGFKIAT<HLINHTSEPKYK

Parental  SRYRTAAESSLYSCYRNVLQLAKEQSMSSVGFCVINSAKRGYP-LEDATHIALRTVRRFLEIHGETI-EK
          S.Y.TA.E.SL..C.R...Q....Q...........SAK..YP.LE..T..AL..VR.FLEI..ET...K
Retrocopy SHYPTAPEGSL*GC*RRIVQKKSSQCLRLHSVSSV-SAKQIYP<LENETYTALCIVRKFLEIYEETT<KK

Parental  VVFAVSELEEATYQKLLPLYFPRSLKEECRSLPYLPADIGNAEGEPVVPERQIRISEKPG
          V.FAVS.L..ATYQ.L....F.RSLKE..RS.PYLP.D..N.E...V.P...IRISEK.G
Retrocopy VRFAVSKLKVATYQELPLPEFSRSLKES-RSQPYLPEDVENVERWTVGPKGKIRISEKLG

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
SRP017611_brain	0.00 RPM	18.36 RPM
SRP017611_kidney	0.00 RPM	10.10 RPM
SRP017611_liver	0.00 RPM	8.19 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1125 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1125 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012907	2 retrocopies	retro_chof_1607, retro_chof_2559,
Echinops telfairi	ENSETEG00000004391	1 retrocopy	retro_etel_530,
Felis catus	ENSFCAG00000003468	1 retrocopy	retro_fcat_1125 ,
Mus musculus	ENSMUSG00000027865	1 retrocopy	retro_mmus_2225,