RetrogeneDB ID: retro_fcat_615

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:54768475..54769928(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKAP2L
• Ensembl ID: ENSFCAG00000028904
• Aliases: None
• Description: cytoskeleton associated protein 2-like [Source:HGNC Symbol;Acc:26877]

Sequence

>retro_fcat_615
GCTCATAGTCAAACCAAGAGCAGTTTGGCTCCTAAACAAGCCTTGGGCAAAAGTTCAGGGAATAGTGCTGTTTTGAAAGA
CAGAGCTAGTAAACAATTTGTTGGAGAAACACAAATTAGGATCCCACCCGTACAGTCACAGCAACTCTCTAGAGGAACAA
ATCTTGCAAGACCAGGGGAAAAACTCCCAAAGACAGTTTCCTCTCACTATGTTCAGACCCTTAGTAGGACTCGAGCATCA
AAGAAACCAGTGGTCGAAGACATAAAGGATATAAAGATTAATAGAGATAAATATGAAAAACCAAATGAAGCTAAGTTATA
GTCACACACTATTACTGCGAAGAAAGTAAAACAAACCAAACCCTGGACATGCCCCAGTGTGTTTCTGGGAGGCTATACCA
GCAGACATCTAAACATCAAGCAAAATCAGAAATCTACTCAACCTTGTTTTAAACCTCAGACATCACATGCACTGCAAAAG
TCAAAAGCCATAAGCCAAAGTTCTAATTTGACAGTTGGCAGTTCCAATTCAGTCATTCCAAGCACCCCTAACATAACAGC
AAATGGAACCAGTGGGAATAAATGCAGCAGTGGCTATCAACAAAAAGCACAGACTTTGGACTCCAAGTTGAAAAAAATTC
TTCCCCAGAACCATTTTCTCAATAAGACAGCTCCCAAAACTCAAGCTGGTAACAAAACCATAAATGGAAGAAGAGTCCCA
AATGGGACCCAAATTAATCCAAATATTAGGAAGAAGATCACAGCAGAGGATCAAAGGAAACACCTGGATGAATGGCAGAA
ATCTAAGGGGAATGTCTATAAATGGCCTCCTATGGAAGTTGAAACAAAAAGAAAAATAGAGGAAATGAATATTTCATTCT
GGAAGAGTATGGAAAAACATGAAGAAAAGAATGCACCACTTGCACTGTCCAAAAAAATTTAACTACACTCCAACAGTGTC
TGCAGCTCATTGAAGGGGTGTACGTTCTAATGAAATATTTATCATATTGCCTAGTTTTCCTAAGGCTGAAAATTTTCCTA
AATTCTGAATCTGCAAAGCAAAGTTGTCGCCAAGTAAAAGCACCTTTGATGTTATTGAGCTGTAAGAAAAGGCCATTCGA
AACGGGGCAACACGGACATAAGAGTTGCCAAGAAGTTGTTCTTCATAATTTGTAAGACCCAAACAGAATCACAGGACTTA
CCTCTGACTCTTTGTTTGCTGAAACAGATAGAACATCAATAGAAGAGCCGGGCGTAAGATGGAATCTGAAAAGTCTTGTC
TTTCTCTAAAAGAGAGAGAAGAGTTTACAGCAACACCCCAAATAACCAAGACAGAAGAAGATCCTCATCTTGGTATCAAA
TTACAGATCACCTGGATCCCTAAAATAAGTGGAATGCCAGAAGTGCAAGGCTTGAAGGTCCTCACTGTTGTAAGGCGTTC
AGCAAGGAGTGAG

Alignment

ORF - retro_fcat_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.15 %
• Parental protein coverage: 64.98 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SYNQTKSSLAPKQALGKSSGNSAFLKDRVNKQFVGKTQIRIPPVKSQQLSRGTNLARPGEKLPKTAPYHY
          ...QTKSSLAPKQALGKSSGNSA.LKDR..KQFVG.TQIRIPPV.SQQLSRGTNLARPGEKLPKT...HY
Retrocopy AHSQTKSSLAPKQALGKSSGNSAVLKDRASKQFVGETQIRIPPVQSQQLSRGTNLARPGEKLPKTVSSHY

Parental  VQTLSRTQASRKPVVKDIKDIKVNRGKYERPNETKVQSHTVTEQKVKHTKPRTCPSVLPGGCNNRHPNTR
          VQTLSRT.AS.KPVV.DIKDIK.NR.KYE.PNE.K..SHT.T..KVK.TKP.TCPSV..GG...RH.N..
Retrocopy VQTLSRTRASKKPVVEDIKDIKINRDKYEKPNEAKL*SHTITAKKVKQTKPWTCPSVFLGGYTSRHLNIK

Parental  QDQKSTQPCCRPRTSCALQKSKAISQRPNLIVGTFNSVVPSTPNITANGTNGNRCSNSCQQKAQILDTKL
          Q.QKSTQPC..P.TS.ALQKSKAISQ..NL.VG..NSV.PSTPNITANGT.GN.CS...QQKAQ.LD.KL
Retrocopy QNQKSTQPCFKPQTSHALQKSKAISQSSNLTVGSSNSVIPSTPNITANGTSGNKCSSGYQQKAQTLDSKL

Parental  KKTLPQNHFLNKTAPKTQAGNKTIHGGRVPNGTQTNPNIKKKITAEDRRKQLEEWQKSKGKIYKRPPMEL
          KK.LPQNHFLNKTAPKTQAGNKTI.G.RVPNGTQ.NPNI.KKITAED.RK.L.EWQKSKG..YK.PPME.
Retrocopy KKILPQNHFLNKTAPKTQAGNKTINGRRVPNGTQINPNIRKKITAEDQRKHLDEWQKSKGNVYKWPPMEV

Parental  KTKRKIIEEMNISFWKSMEKEDEEKKAQLELSNKI-NNTLTECLQFIE-RGMLSNEVFTILSSIPEAKKF
          .TKRK.IEEMNISFWKSMEK..EEK.A.L.LS.KI...TL..CLQ.IE.RG..SNE.F.IL.S.P.A..F
Retrocopy ETKRK-IEEMNISFWKSMEKH-EEKNAPLALSKKI<LTTLQQCLQLIE<RGVRSNEIFIILPSFPKAENF

Parental  AKFWICKAKLLASKGTFDVIGLYEEAIRNGATPIQEL-REVVLNILQDTNRTTEGVTSDSSVAEMNITSI
          .KF.ICKAKL..SK.TFDVI.L.E.AIRNGAT...EL..EVVL..L.D.NR.T.G.TSDS..AE...TSI
Retrocopy PKF*ICKAKLSPSKSTFDVIEL*EKAIRNGATRT*EL>QEVVLHNL*DPNRIT-GLTSDSLFAETDRTSI

Parental  EE-LANKTESEKSCLSLKEREQVTGTPQITKAEQDNHPGIKLQVAPIPRISGIAEVHDMKLITPVRRSAR
          EE....K.ESEKSCLSLKERE..T.TPQITK.E.D.H.GIKLQ...IP.ISG..EV...K..T.VRRSAR
Retrocopy EE<AGRKMESEKSCLSLKEREEFTATPQITKTEEDPHLGIKLQITWIPKISGMPEVQGLKVLTVVRRSAR

Parental  IE
          .E
Retrocopy SE

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	0.34 RPM
SRP017611_kidney	0.00 RPM	0.93 RPM
SRP017611_liver	0.00 RPM	1.52 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_615 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_615 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007242	1 retrocopy	retro_cfam_858,
Cavia porcellus	ENSCPOG00000010435	2 retrocopies	retro_cpor_229, retro_cpor_528,
Felis catus	ENSFCAG00000010021	1 retrocopy	retro_fcat_1770,
Felis catus	ENSFCAG00000028904	1 retrocopy	retro_fcat_615 ,
Mustela putorius furo	ENSMPUG00000009729	1 retrocopy	retro_mputfur_1172,
Ochotona princeps	ENSOPRG00000012796	1 retrocopy	retro_opri_904,
Tupaia belangeri	ENSTBEG00000013625	2 retrocopies	retro_tbel_1637, retro_tbel_4436,