RetrogeneDB ID: retro_fcat_1960

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:125779974..125780637(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPB
• Ensembl ID: ENSFCAG00000014447
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptides B and B1 [Source:HGNC Symbol;Acc:11153]

Sequence

>retro_fcat_1960
TTCAAAGCTTTTGGCCAGCTTATGAATTTGATCTTCTGTGACTGTGAAGAATTCAGGAAGATCTAGCCAAAGAACTCAAA
ACAAGCAGAAAGAGAAGAGAAGTGACTCCTCGGTCTGGTGCTACTTTGGGGAGAGAAGCTAGTGTCAATGACAGTAGACG
GGTCTACTCCCAAAGATACTGGCATTGCACGACTATCACTTGCTGGAGCTGCCAGGGACCCAGGGATAGGGAGAGCTCTG
GGCAGAGGAATCCCCACTGGTGTTCTGATGCCCTACACTCCCGTAGGACTTGCTGGGCCAGTCTGAGGGCCATCCCAACA
AGTGACGACCCGGCAAGGAAGAGGCACTGTGGCAGCCGCTGGAGCTACTGCCACAGTCAGAACTGGAGGGGCCCCAACCC
AATATCTACCTGGCTGTGGGGTCCTTCACACCTATGGGCTGAGGGCACCCCCTGCAGGCACTATGGGCCCACCACCTGTC
ATGAGGACTCCCATGGGTTCCCCAATGGGGATCCCCTTCTGGACAAGGAACTCCAATTGGCATGCTCCCACCAGGGATGC
AGCCCCCTTCTTCCAGGGGTTTGAGGCCTTCTTTGACCCTTGGCCACAGAGTTATGGAAATTGCTCCACAGAGGCATGGG
CCCAGTGCTCCAGGGCCACATTG

Alignment

ORF - retro_fcat_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 71.34 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  FKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGA
          FKAF...MNLI.CDC.EFRKI.PKNSKQAEREEK..LGLVLL.GE.LVSMTV.G..PKDTGIAR..LAGA
Retrocopy FKAFGQLMNLIFCDCEEFRKI*PKNSKQAEREEK*LLGLVLLWGEKLVSMTVDGSTPKDTGIARLSLAGA

Parental  AGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPP
          A..PGIGRA.GRGIP.GV.MP..P.GLAGPV.G...PSQQV.T.QGRGTVAAA.A.AT....GAPTQY.P
Retrocopy ARDPGIGRALGRGIPTGVLMPYTPVGLAGPV*G---PSQQVTTRQGRGTVAAAGATATVRTGGAPTQYLP

Parental  GRG-GPP-PPMGRG-APPPGMMGPPPGMRPPMGPPMGI-PPGRGTPMGMPPPGMRPPP-PGM-RAFFDPW
          G.G.GP...PMG.G.APP.G.MGPPP.MR.PMG.PMGI.P.G.GTP.GM.PPGM.PP..PG...AFFDPW
Retrocopy GCG<GPS<TPMG*G<APPAGTMGPPPVMRTPMGSPMGI>PSGQGTPIGMLPPGMQPPS>PGV>EAFFDPW

Parental  PQSYGSSSTEAWARLPQTCL
          PQSYG..STEAWA......L
Retrocopy PQSYGNCSTEAWAQCSRATL

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	15.04 RPM
SRP017611_kidney	0.00 RPM	28.65 RPM
SRP017611_liver	0.00 RPM	14.35 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1960 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1960 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 17 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011353	1 retrocopy	retro_amel_1403,
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Dasypus novemcinctus	ENSDNOG00000007896	2 retrocopies	retro_dnov_2060, retro_dnov_2471,
Erinaceus europaeus	ENSEEUG00000015568	3 retrocopies	retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus	ENSFCAG00000014447	2 retrocopies	retro_fcat_1788, retro_fcat_1960 ,
Felis catus	ENSFCAG00000022298	2 retrocopies	retro_fcat_1390, retro_fcat_1895,
Microcebus murinus	ENSMICG00000016519	4 retrocopies	retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861,
Myotis lucifugus	ENSMLUG00000016951	1 retrocopy	retro_mluc_1725,
Mustela putorius furo	ENSMPUG00000009283	1 retrocopy	retro_mputfur_1153,
Nomascus leucogenys	ENSNLEG00000009206	1 retrocopy	retro_nleu_761,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Ochotona princeps	ENSOPRG00000007459	2 retrocopies	retro_opri_697, retro_opri_72,
Pongo abelii	ENSPPYG00000010841	1 retrocopy	retro_pabe_2265,
Pteropus vampyrus	ENSPVAG00000017013	1 retrocopy	retro_pvam_289,
Tupaia belangeri	ENSTBEG00000010040	3 retrocopies	retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta	ENSTSYG00000014498	2 retrocopies	retro_tsyr_45, retro_tsyr_719,