RetrogeneDB ID: retro_fcat_1037

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:67831860..67832653(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSFCAG00000000279
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]

Sequence

>retro_fcat_1037
CAAAAACAGTCTGAACTTGATCAAGATCTGGATGATGTTGAAGAAATAGAAGAAGAAACTGGCAAAGAAACAAAAATCAA
AGCATGTCAGCTGACTGTTCAAATGATGCAAAATCCTCATATTATTGTAACCCTTGAAATAAAACTTGATGGTCTGATAG
AAACACCAGCAGGATACATTGAGAACTTGCCTAGGGTAGTTAAAAGACGAGTGAATACTCTCAAAAACGGTAAGTTAGGT
GTGCAAAAATAGAAGCCAAGTTCTATGAGGAAGCTGATGGTCTTGAAAGGAAGTATGCTGTGCTCTGCTGGCCTCTATTT
GATAGTGACTTGAGATCATTAATCCAACTTATGAACCTATGGAAGAATGTGAATAGAAACTGGATGAGGAAAATGAAATT
TTGTAGAAGCTGAAAGGAAAGCCAAGAATAAAGATGAGAAAAAGGATGAAGAAAAAGAAGACTCCAAGATAATTCCTGAA
TTCTGGGTGACTGTTTTTAAGAATGTTGACTTGTTCAATGATATGGTTCAGGAATATGATGAACCTATTCTGAAGCACTT
GAAAGATATTAAAGTGAAGTTCTCAGATACTGACCAGCCCCTGACGTTTGTCTGAGAATTCCACTTTGAACCCAGTGAAC
ATTTCACAAGTGGAAGTGTTCACAAAGACATATACGATGAAATCAGAAGCAGATGATTCTGATCCCTTTTCTTTAGATGG
ACCAGAAATTATGGGTTGTACAGGGTGCCAGATAGATTGGGAAAATGGAAAGAATGTCACTTTGAAAACCATT

Alignment

ORF - retro_fcat_1037 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.28 %
• Parental protein coverage: 68.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESLPRVVKR
          ..QSELDQDLDDVEE.EEE.TG.ETKIKA.QLTVQMMQNP.I...L...LDGL.ETP.GYIE.LPRVVKR
Retrocopy QKQSELDQDLDDVEEIEEE-TGKETKIKACQLTVQMMQNPHIIVTLEIKLDGLIETPAGYIENLPRVVKR

Parental  RVNALKNLQ-VKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRF-EIINAIYEPTEEECEWKPDEEDEISE
          RVN.LKN...V.CA.IEAKFYEE...LERKYAVL..PLFD....EIIN..YEP.EE.CE.K.DEE.EI..
Retrocopy RVNTLKNGK<VRCAKIEAKFYEEADGLERKYAVLCWPLFDSDL<EIINPTYEPMEE-CE*KLDEENEIL*

Parental  ELK-EKAKIEDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSFV
          .LK..KAK..DEKKDEEKED.K.IPEFW.TVFKNVDL..DMVQE.DEPILKHLKDIKVKFSD..QP..FV
Retrocopy KLK<RKAKNKDEKKDEEKEDSKIIPEFWVTVFKNVDLFNDMVQEYDEPILKHLKDIKVKFSDTDQPLTFV

Parental  LEFHFEPNEYFTN-EVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTI
          .EFHFEP.E.FT..EV.TKTY.M.SE.DDSDPFS.DGPEIMGCTGCQIDW..GKNVTLKTI
Retrocopy *EFHFEPSEHFTS>EVFTKTYTMKSEADDSDPFSLDGPEIMGCTGCQIDWENGKNVTLKTI

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	147.71 RPM
SRP017611_kidney	0.00 RPM	126.55 RPM
SRP017611_liver	0.00 RPM	43.47 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1037 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1037 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 15 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Felis catus	ENSFCAG00000000279	1 retrocopy	retro_fcat_1037 ,
Homo sapiens	ENSG00000187109	3 retrocopies	retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Nomascus leucogenys	ENSNLEG00000004682	4 retrocopies	retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pan troglodytes	ENSPTRG00000005240	4 retrocopies	retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Vicugna pacos	ENSVPAG00000007290	3 retrocopies	retro_vpac_435, retro_vpac_441, retro_vpac_601,