RetrogeneDB ID: retro_cfam_1086

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:50435386..50436327(-)
• Located in intron of: ENSCAFG00000005857

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRPDL
• Ensembl ID: ENSCAFG00000008940
• Aliases: None
• Description: None

Sequence

>retro_cfam_1086
ACGCTCCGCCGCCGACCCCGGCCGCCAGCTCCGCCACCATGGAGGACATGAACGAGTACAGCAACATAGAGGAGTTCGCA
GAGGGATCCAAGATCAACGCGAGCAAGAATCAGCAGGATGACGGTAAAATGTTTATTGGAGGCTTGAGCTGGGATACAAG
CAAGAAAGATCTGACTGAATATTTGTCTCGATTTGGGGAAGTTGTAGACTGTACAATTGAAACAGTTCCAGTGACTGGAA
GACCAAGAGGATTTGGATTTGTGCTTTTCAAAGATGCTGCTAGTGTTGATAAGGTTTTGGAACTGAAAGAACACAAACTG
GATGGCAAGTTGATAAACCCCAAAAGGGCCAAAGCTTTAAAAGGGAAAGAACCCCCCAGAAAGATTTTTGTGGGTGGATT
GAGCCCAGATACTTGTGAAGAACAAATTAAAGAATATTTTGGAGCCTTTGGAGAGATTGAATATATTGAACTTCCCATGG
ATACAAAAACAAACGAAAGAAGAGGATTTTGTTTTATTACCTATACAGACGAAGAGCCAGTAAAGGAATTGTTAGAAAGC
AGATATCATCAAATTGGTTCTGGGAAGTGTGAAATCAAAGTCGCACAACCCAAAGAGGTATATAGGCAGCAACAGCAACA
ACAAAAAGGAGGAAGAGGTGCTGCAGCTGGTGGACGAGGTGGTACTAGGGGTCGTGGACGAGGTCAGGGTCAAAACTGGA
ACCAAGGATTTAATAACTATTATGATCAAGGATATGGAAATTACAATAGTGCCTATGGTGGTGATCAAAACTATAGTGGC
TATGGCGGCTATGATTATACTGGGTATAACTATGGGAACTATGGATATGGACAGGGATATGTAGACTACAGTGGCCAACA
GAGCACTTACGGCAAGGCGTCTAGAGGGGGTGGCAGTTACCAAAACAATTACCAGCCATAC

Alignment

ORF - retro_cfam_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.97 %
• Parental protein coverage: 74.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TARQHP-PADNSAAMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGGLSWDTSKKDLTEYLSRFGEVV
          T.R..P.PA..SA.MEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGGLSWDTSKKDLTEYLSRFGEVV
Retrocopy TLRRRP<PAASSATMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGGLSWDTSKKDLTEYLSRFGEVV

Parental  DCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKEPPKKVFVGGLSPDTS
          DCTI.T.PVTGR.RGFGFVLFKDAASVDKVLELKEHKLDGKLI.PKRAKALKGKEPP.K.FVGGLSPDT.
Retrocopy DCTIETVPVTGRPRGFGFVLFKDAASVDKVLELKEHKLDGKLINPKRAKALKGKEPPRKIFVGGLSPDTC

Parental  EEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGSGKCEIKVAQPKEVYR
          EEQIKEYFGAFGEIE.IELPMDTKTNERRGFCFITYTDEEPVK.LLESRYHQIGSGKCEIKVAQPKEVYR
Retrocopy EEQIKEYFGAFGEIEYIELPMDTKTNERRGFCFITYTDEEPVKELLESRYHQIGSGKCEIKVAQPKEVYR

Parental  QQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYNSAYGGDQNYSGYGGYDYTGYNYG
          QQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYNSAYGGDQNYSGYGGYDYTGYNYG
Retrocopy QQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYNSAYGGDQNYSGYGGYDYTGYNYG

Parental  NYGYGQGYADYSGQQSTYGKASRGGGNHQNNYQPY
          NYGYGQGY.DYSGQQSTYGKASRGGG..QNNYQPY
Retrocopy NYGYGQGYVDYSGQQSTYGKASRGGGSYQNNYQPY

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
SRP012049_cerebellum	8.15 RPM	224.53 RPM
SRP017611_brain	5.32 RPM	111.78 RPM
SRP017611_kidney	3.90 RPM	75.55 RPM
SRP017611_liver	3.26 RPM	57.94 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1086 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1086 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1086 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000241	2 retrocopies	retro_cfam_408, retro_cfam_412,
Canis familiaris	ENSCAFG00000006580	16 retrocopies	retro_cfam_1080, retro_cfam_1081, retro_cfam_1170, retro_cfam_1323, retro_cfam_1616, retro_cfam_1844, retro_cfam_2017, retro_cfam_2128, retro_cfam_360, retro_cfam_564, retro_cfam_702, retro_cfam_803, retro_cfam_839, retro_cfam_855, retro_cfam_892, retro_cfam_937,
Canis familiaris	ENSCAFG00000008940	1 retrocopy	retro_cfam_1086 ,
Canis familiaris	ENSCAFG00000013497	12 retrocopies	retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272, retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Dipodomys ordii	ENSDORG00000000968	1 retrocopy	retro_dord_145,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Nomascus leucogenys	ENSNLEG00000008636	1 retrocopy	retro_nleu_673,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,