RetrogeneDB ID: retro_fcat_1568

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D3:83167515..83168248(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSFCAG00000000455
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_fcat_1568
CAATATTTGTCTCGATTTGGGAAAATTGTAGACTGTACAATAAAAACAGATCCAGTGACTGGAAGCTCGAGAGGATTTGG
ATTTGTGCTTTTCAGAGATGCTGCTAGTGTTGATACGGTTTGGGAACTGAAAGAACACAAACTGGATGGCAAATTAATAG
ACCCCCAAAGGGGCCAGAGCTTTAAAAGGGAAAGAACCTCCCAAAAAGATGTTTGTGGGTGGATTGAGCCAAGGTACTTC
TGAAGAACAAACTGAAGAATATTTTGGAGCCTTTGTAGATATTGAAAATACTGCACTTCCCGTGGAGACAAAACCAAATG
AAAGAGGACTTTGCTTTATCACATATACCGATGAAGAGCCAGGAAAGAAATTGTTAGAAAGCAGATATCATCAAATTGGT
TCTGGGAAGTGTGAAATCCAAGTTGCACAACCCAACGAGGTCTATAGGCAGCAACAGCAACAACAAAAAGGAGAAAGAGG
TGCAGTGGCTGGTGGACAAGGTGGTACTAGGGGTCATGGGCAAGGTCAGGGCCAAAACTGGAACCAGGGATTTAATAACT
GTTATGATCAAGGGTATGGAAATTACGATAGTGCCTTTGGTGGTGACCGAAACTATAGTGGCTGTGGCTGTGATTATACC
GGGTATAACTAGGGAGACTATGGATATGGACACAGATATGCAGACTACAGTGGCCAACAGAGCACTTATGGCAAGGCTTC
TCGAGGGGGTGGC

Alignment

ORF - retro_fcat_1568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 58.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKR-AKALKGKEPPKK
          .YLSRFG..VDCTIKTDPVTG.SRGFGFVLF.DAASVD.V.ELKEHKLDGKLIDP.R.A.ALKGKEPPKK
Retrocopy QYLSRFGKIVDCTIKTDPVTGSSRGFGFVLFRDAASVDTVWELKEHKLDGKLIDPQR>ARALKGKEPPKK

Parental  VFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGSGKCE
          .FVGGLS..TSEEQ..EYFGAF..IEN..LP..TK.NER.G.CFITYTDEEP.KKLLESRYHQIGSGKCE
Retrocopy MFVGGLSQGTSEEQTEEYFGAFVDIENTALPVETKPNER-GLCFITYTDEEPGKKLLESRYHQIGSGKCE

Parental  IKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYNSAYGGDQNYSGY
          I.VAQP.EVYRQQQQQQKG.RGA.AGG.GGTRG.G.GQGQNWNQGFNN.YDQGYGNY.SA.GGD.NYSG.
Retrocopy IQVAQPNEVYRQQQQQQKGERGAVAGGQGGTRGHGQGQGQNWNQGFNNCYDQGYGNYDSAFGGDRNYSGC

Parental  GGYDYTGYNYGNYGYGQGYADYSGQQSTYGKASRGGG
          .G.DYTGYN.G.YGYG..YADYSGQQSTYGKASRGGG
Retrocopy -GCDYTGYN*GDYGYGHRYADYSGQQSTYGKASRGGG

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	131.76 RPM
SRP017611_kidney	0.00 RPM	82.76 RPM
SRP017611_liver	0.00 RPM	51.66 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1568 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1568 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 11 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568 ,
Felis catus	ENSFCAG00000010150	9 retrocopies	retro_fcat_1574, retro_fcat_1742, retro_fcat_1867, retro_fcat_382, retro_fcat_474, retro_fcat_712, retro_fcat_781, retro_fcat_844, retro_fcat_888,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Felis catus	ENSFCAG00000027765	1 retrocopy	retro_fcat_692,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,