RetrogeneDB ID: retro_ocun_1248

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:2156899..2157463(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000006242
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPA1
• Ensembl ID: ENSOCUG00000017417
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide A' [Source:HGNC Symbol;Acc:11152]

Sequence

>retro_ocun_1248
GCGGCGCAGTACACCGACGCCATGCGGGACTGCGAGCTGGACCTCCGTAGGTATAAAATTCCTGTCATTGAAAACCTGGG
TGCTACCTTGGACCAGTTTGATGCTATTGACTTTTCTGACAATGAGATCAGGAAGCTGGATGGGTTTCCTTTATTGAGAA
GATTGAAAACGTTATTAGTGAACAACAGAATATGCCGTATAGGTGAGGGGCTTGCTCAGGCTCTGCCCTGTCTCACAGAA
CTCATTCTCACTCACAACAGTCTTGGGGAACTGGGCGACCTGGACCCCTTGGCCTCCCTCAGATCGCTGACTTACCTAAG
TATTCTACGAAATCCTGTAACAGACAAGAAGCATTACAGACTGTATGTAATTTACAAAGTTCCACAAGTCAGAGTACTGG
ATTTCCAGCAAGTAAAACTAAAAGAGCGTCAGGAAGCAGAGCAAGTGTTCAAGGGCAAACGGGGTGCACAGCTTGCAAAG
GAAACTGCCAGGAGAAGCAAAACTTTTAATCCAGGGGCTGGTTTGCCAACTGACAAAAAGAAAGGTGGGCCGGCTCCAGG
GGAG

Alignment

ORF - retro_ocun_1248 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.77 %
• Parental protein coverage: 74.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVQYTHDVLDRDAEHAGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLLVNNNRICRIGE
          A.QYT....D.......YKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLLVNN.RICRIGE
Retrocopy AAQYTDAMRDCELDLRRYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLLVNN-RICRIGE

Parental  GLDQALPCLTELILTNNSLMELGDLDPLASLRSLTYLSILRNPVTNKKHYRLYVIYKVPQVRVLDFQKVK
          GL.QALPCLTELILT.NSL.ELGDLDPLASLRSLTYLSILRNPVT.KKHYRLYVIYKVPQVRVLDFQ.VK
Retrocopy GLAQALPCLTELILTHNSLGELGDLDPLASLRSLTYLSILRNPVTDKKHYRLYVIYKVPQVRVLDFQQVK

Parental  LKERQEAEKMFKGKRGAQLAKDIARRSKTFNPGAGLPADKKKGGPSPGD
          LKERQEAE..FKGKRGAQLAK..ARRSKTFNPGAGLP.DKKKGGP.PG.
Retrocopy LKERQEAEQVFKGKRGAQLAKETARRSKTFNPGAGLPTDKKKGGPAPGE

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	0.28 RPM	31.07 RPM
SRP017611_kidney	0.00 RPM	24.43 RPM
SRP017611_liver	0.00 RPM	13.57 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1248 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1248 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007128	1 retrocopy	retro_amel_850,
Bos taurus	ENSBTAG00000013593	1 retrocopy	retro_btau_1453,
Canis familiaris	ENSCAFG00000010564	1 retrocopy	retro_cfam_1208,
Echinops telfairi	ENSETEG00000010019	1 retrocopy	retro_etel_1366,
Felis catus	ENSFCAG00000018594	1 retrocopy	retro_fcat_322,
Homo sapiens	ENSG00000131876	2 retrocopies	retro_hsap_2148, retro_hsap_2601,
Loxodonta africana	ENSLAFG00000012638	1 retrocopy	retro_lafr_1230,
Myotis lucifugus	ENSMLUG00000014213	1 retrocopy	retro_mluc_2442,
Mustela putorius furo	ENSMPUG00000010938	1 retrocopy	retro_mputfur_1139,
Oryctolagus cuniculus	ENSOCUG00000017417	3 retrocopies	retro_ocun_1248 , retro_ocun_1775, retro_ocun_366,
Pan troglodytes	ENSPTRG00000007513	1 retrocopy	retro_ptro_1525,
Tupaia belangeri	ENSTBEG00000001669	2 retrocopies	retro_tbel_1772, retro_tbel_3447,
Tarsius syrichta	ENSTSYG00000003965	2 retrocopies	retro_tsyr_1229, retro_tsyr_1943,