RetrogeneDB ID: retro_fcat_236

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:77054571..77055059(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIH1D2
• Ensembl ID: ENSFCAG00000000608
• Aliases: None
• Description: PIH1 domain containing 2 [Source:HGNC Symbol;Acc:25210]

Sequence

>retro_fcat_236
TCATCCTGAAAGGGTCTGCTTGCTCAGGTCAGTGAGCTCCGGAGCCTCCCAGACGTGCCGGCCGGAGGCAACACCAGAGC
CGTGAGCAGTTCACTCAACAGCCGCTGGAAGAGGGGAGATGGCTCTATTCTGCCCCAGAACCGCAGCTCTCTGTCTACAA
ACCAGGGTCCCCAAAACGAAAGAAGAAAATCCTTTCTATCAAACTTTGTCAGTTGGAAAGGGCCCCAGCTCCCCAGTCAA
CCACTCATCCAGCACCTCTAAGTGCCGGCCGGCCAGCCGCTGTGTCTGAGACGTTGCGTGTTTATACAGTTGTTGATGTT
GCCTACAATCCTGGTGTCCTCCAGGCAGCAGAAAAGCACCACGTGAAAAAAGATCAGTTAGTACAGATGACCATGAAATG
CATTGAGGAATTCCAATGTATTCTCTCACACTCTTACAGTATTCCTAAATTTAGAATCAAAGGAAGCATCCAAAGCGTGA
AACAAAAT

Alignment

ORF - retro_fcat_236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.87 %
• Parental protein coverage: 52.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSSKGLLTQVTQFWNLLDDLAESNP-EGYEKFIQQQLKE-GEQLCAAPEPW-LCLQTRILKPKE-KILFI
          SS.KGLL.QV.....L.D..A..N.....E.F.QQ.L.E.GE.....P....LCLQTR..K.KE.KIL.I
Retrocopy SS*KGLLAQVSELRSLPDVPAGGNT<QSREQFTQQPLEE<GEMALFCPRTAALCLQTRVPKTKE>KILSI

Parental  NLCQWKRIPAPQSNTHPVPLSIGRPEDRSETSDVYTVIDVAYNPDVLQAAEKDQVKKDQLIQMAMKCIEE
          .LCQ..R.PAPQS.THP.PLS.GRP...SET..VYTV.DVAYNP.VLQAAEK..VKKDQL.QM.MKCIEE
Retrocopy KLCQLERAPAPQSTTHPAPLSAGRPAAVSETLRVYTVVDVAYNPGVLQAAEKHHVKKDQLVQMTMKCIEE

Parental  KLQFTLSHSYSITNFRIKGSIQRMKQN
          ..Q..LSHSYSI..FRIKGSIQ..KQN
Retrocopy -FQCILSHSYSIPKFRIKGSIQSVKQN

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	6.31 RPM
SRP017611_kidney	0.00 RPM	6.90 RPM
SRP017611_liver	0.00 RPM	0.81 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_236 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_236 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004081	1 retrocopy	retro_amel_444,
Felis catus	ENSFCAG00000000608	1 retrocopy	retro_fcat_236 ,
Pteropus vampyrus	ENSPVAG00000009619	1 retrocopy	retro_pvam_1235,