RetrogeneDB ID: retro_fcat_1352

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:79860897..79862165(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000006328
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MPP1
• Ensembl ID: ENSFCAG00000006578
• Aliases: None
• Description: membrane protein, palmitoylated 1, 55kDa [Source:HGNC Symbol;Acc:7219]

Sequence

>retro_fcat_1352
AGTGTGACCTAGGGCATGTACACCAACGGCTGGGCTGCCCCAGGAAGCCTTGCCCAGGCCAAGGGGCAGGACGTACAGAA
GGTGCGACTCATCCAGTTCCAGACAGTCACCCAAGAGCCCATGGGAATCATCCTGAAGCTGAACGACAAGCAGTCCTGTA
CGGTGGCCAGAATTCTTGATGGCGGCATGATTCACAGACAAGGCTCCCTTCACGTTGGGGATGAGAGCCTAGAAATCAAT
GGCACAAACGCGACTAATCACTCAGGAGAGCGGCTGCAGAAGGCGATGAAAGAAACCAAAGGAACGATCTCATTAAAAGT
AATTCCCAACCACCAGAATCATCTTCCTGCACTACAGATGGTCATGAGAGCCAAATTTGACTATGACCCCAAAAAGGACC
ACCTGATCCCCTGGAAGGAGGCGGGGCTGAAGTTTGTTACCGGGGACATCATCAAGATACTCAGCAAAGACGACAGTAAC
TGGTGGCAAGGGCAGGTGGAAGCTTCCTCCAAGGAGTCAGCTGGATTGATCCTTTCTCCTGAGCTGCAGGAATGGCGAGT
GGCAAGCGTGGCTCAGTCTGCTGCGAGCGAAGCCCCAAGCTGCAGTCCCTTCGGGAAGAAGTACAAAGACCAGTACCTGG
CCAAGCACAGCTCGATTTTTGACCAGTTGGAGGTCGTTTCCTACGAGGAAGCTGGTCGGCTCCCGGCGTTCATGAAGAAG
ACCCTGGTGCTTATAGGAGCCAGCGGGGTGGGCCGCTGCCACATTAAGAGTGCCCTGCTCAGCCAGAACCTGGACAAGTT
TGCGTACCCCACCCCGTGTACCACACGGGCGCCCAGGAAGAGTGGGGAAGATGGGGAAAATACCACTTTGTCTCCACCGA
AGAGATGACGAGGGGCATCTCTGCCAACGAATTCCTGGAGTTTGGCAGCTACCAGGGCAACGTGTTTGGCACCACATTTG
AAACCCTGCACCAGATTCATAAGCAGGACAGGATTGCCATCCTGGACATTGAGCCCCAGACCCTGAAGATTGTCTGCACA
GCAGAACTGTCATCGTTCATTGTGTTCATCGCACCCTCCGACCAGGGGGCACAGACAGAGGCCCTGCAGCAGCTGCAGAA
AGACTCCGAGGCCATCCGCAGCCACTATGCGTACTACTTTGACCTCTCGCTGGTCGACAACGGCGTCGATGAAACCCTGA
AGAAATTGCAAGAAGCCTTGGAGCAGGCGTGCAGTTCTCCACAGTGCGTGCCTGTCTCCTGGGTTTAC

Alignment

ORF - retro_fcat_1352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.45 %
• Parental protein coverage: 98.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AMTEDMYTNGCAAPGSPAQAKGQDVRKVRLIQFEKVTEEPMGITLKLNDKQSCTVARILHGGMIHRQGSL
          ..T..MYTNG.AAPGS.AQAKGQDV.KVRLIQF..VT.EPMGI.LKLNDKQSCTVARIL.GGMIHRQGSL
Retrocopy SVT*GMYTNGWAAPGSLAQAKGQDVQKVRLIQFQTVTQEPMGIILKLNDKQSCTVARILDGGMIHRQGSL

Parental  HVGDEILEINGTNVTNHSVDQLQKAMKETKGMISLKVIPNQQNRLPALQMFMRAQFDYDPKKDHLIPCKE
          HVGDE.LEINGTN.TNHS...LQKAMKETKG.ISLKVIPN.QN.LPALQM.MRA.FDYDPKKDHLIP.KE
Retrocopy HVGDESLEINGTNATNHSGERLQKAMKETKGTISLKVIPNHQNHLPALQMVMRAKFDYDPKKDHLIPWKE

Parental  AGLKFVTGDIIKIINKDDSNWWQGRVEGSSKESAGLIPSPELQEWRVASVAQSAPSEAPSCSPFGKKKKY
          AGLKFVTGDIIKI..KDDSNWWQG.VE.SSKESAGLI.SPELQEWRVASVAQSA.SEAPSCSPFG..KKY
Retrocopy AGLKFVTGDIIKILSKDDSNWWQGQVEASSKESAGLILSPELQEWRVASVAQSAASEAPSCSPFG--KKY

Parental  KDKYLAKHSSIFDQLDVVSYEEVVRLPAFKRKTLVLIGASGVGRSHIKSALLSQNPDKFAYPAPYTTRPP
          KD.YLAKHSSIFDQL.VVSYEE..RLPAF..KTLVLIGASGVGR.HIKSALLSQN.DKFAYP.P.TTR.P
Retrocopy KDQYLAKHSSIFDQLEVVSYEEAGRLPAFMKKTLVLIGASGVGRCHIKSALLSQNLDKFAYPTPCTTRAP

Parental  KKSEEDGK-EYHFISTEEMTRDISANEFLEFGSYQGNMFGTKFETVHQIHKQDKIAILDIEPQTLKIVRT
          .KS.EDG...YHF.STEEMTR.ISANEFLEFGSYQGN.FGT.FET.HQIHKQD.IAILDIEPQTLKIV.T
Retrocopy RKSGEDGE<KYHFVSTEEMTRGISANEFLEFGSYQGNVFGTTFETLHQIHKQDRIAILDIEPQTLKIVCT

Parental  AELSPFIVFIAPTDQGAQTEALQQLQKDSEAIRSQYAHYFDLSLVNNGVDETLKKLQEAFERACSSPQWV
          AELS.FIVFIAP.DQGAQTEALQQLQKDSEAIRS.YA.YFDLSLV.NGVDETLKKLQEA.E.ACSSPQ.V
Retrocopy AELSSFIVFIAPSDQGAQTEALQQLQKDSEAIRSHYAYYFDLSLVDNGVDETLKKLQEALEQACSSPQCV

Parental  PVSWVY
          PVSWVY
Retrocopy PVSWVY

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	21.23 RPM
SRP017611_kidney	0.00 RPM	69.05 RPM
SRP017611_liver	0.00 RPM	21.43 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1352 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1352 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004231	1 retrocopy	retro_dnov_977,
Felis catus	ENSFCAG00000006578	1 retrocopy	retro_fcat_1352 ,
Pteropus vampyrus	ENSPVAG00000009226	1 retrocopy	retro_pvam_709,
Tupaia belangeri	ENSTBEG00000011524	2 retrocopies	retro_tbel_4481, retro_tbel_564,