RetrogeneDB ID: retro_cfam_1114

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:2179681..2180221(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004431
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPA
• Ensembl ID: ENSCAFG00000005091
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide A [Source:HGNC Symbol;Acc:11151]

Sequence

>retro_cfam_1114
ATGAGGGGCCAGGCCTTTGTCATCTTCAAGGAAGCCAGCAGCGCCACCAATGCCCTGCCTCCATGCAGGGTTTCCCCTTC
TACGACAAGCCCATGCGCATTCAGTATGCCAAGACTGACTCAGATATTATTGCCAAGATAAAGGGTACCTTCGTGGAGCG
GGACCGCAAGCGGGAGAAGAGGAAGCCCAAAAGCCAGGAGACCCCAGCAGCCAAGAAGACTGTGCAGGGTGGGGCCGCCG
CCCCTGTGGTGGGGGCTCTCCAGGGCCCTGTCCCGGGTATGCCCCCAATGACTCAAGCCCCCCCACATCATGCATCACAT
GCCAGGCCAGCCTCCCTACATGCTGCCTCCTGGCATGATCCCGCCTCCAGACCTGGCACCTAGACAAATCCCACCAGGAG
CCATGCCCCCACAGCAGCTTATGCCGGGGCAGATGCCACCAGCCCAGCCTCTTTCAGAAAATCCACCAAATCACATCTTA
TTCCTCACCAACCTGCCCGAGGAGACCAATGAGCTCATGCCGTCCATGCTTTTCAACCAG

Alignment

ORF - retro_cfam_1114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRGQAFVIFKEVSSATNAL-RSMQGFPFYDKPM---YAKTDSDIIAKMKGTFVERDRKREKRKPKSQETP
          MRGQAFVIFKE.SSATNAL..SMQGFPFYDKPM...YAKTDSDIIAK.KGTFVERDRKREKRKPKSQETP
Retrocopy MRGQAFVIFKEASSATNAL<ASMQGFPFYDKPMRIQYAKTDSDIIAKIKGTFVERDRKREKRKPKSQETP

Parental  AAKKAVQGGAAAPVVGAVQGPVPGMPPMTQAP-RIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ
          AAKK.VQGGAAAPVVGA.QGPVPGMPPMTQAP..IMHHMPGQPPYM.PPGMIPPP.LAP.QIPPGAMPPQ
Retrocopy AAKKTVQGGAAAPVVGALQGPVPGMPPMTQAP>HIMHHMPGQPPYMLPPGMIPPPDLAPRQIPPGAMPPQ

Parental  QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQ
          QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELM.SMLFNQ
Retrocopy QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMPSMLFNQ

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	0.92 RPM	11.72 RPM
SRP017611_brain	0.95 RPM	7.54 RPM
SRP017611_kidney	0.79 RPM	4.42 RPM
SRP017611_liver	0.44 RPM	2.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1114 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1114 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005091	1 retrocopy	retro_cfam_1114 ,
Canis familiaris	ENSCAFG00000005520	4 retrocopies	retro_cfam_1097, retro_cfam_1661, retro_cfam_1689, retro_cfam_264,
Callithrix jacchus	ENSCJAG00000014865	1 retrocopy	retro_cjac_287,
Cavia porcellus	ENSCPOG00000010875	1 retrocopy	retro_cpor_663,
Myotis lucifugus	ENSMLUG00000000219	1 retrocopy	retro_mluc_1517,
Monodelphis domestica	ENSMODG00000007912	1 retrocopy	retro_mdom_447,
Mustela putorius furo	ENSMPUG00000017681	1 retrocopy	retro_mputfur_593,
Mus musculus	ENSMUSG00000061479	6 retrocopies	retro_mmus_275, retro_mmus_3374, retro_mmus_469, retro_mmus_888, retro_mmus_889, retro_mmus_958,
Otolemur garnettii	ENSOGAG00000002864	1 retrocopy	retro_ogar_2046,
Pteropus vampyrus	ENSPVAG00000001494	1 retrocopy	retro_pvam_832,