RetrogeneDB ID: retro_rnor_842

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:84448817..84449377(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccnb1ip1
• Ensembl ID: ENSRNOG00000026056
• Aliases: None
• Description: E3 ubiquitin-protein ligase CCNB1IP1 [Source:RefSeq peptide;Acc:NP_001020312]

Sequence

>retro_rnor_842
TTGGACATTAGCTCCCGAGCACTGGCCTTCTGGACATACCAGGTACACCAGGAACGTCTCTATCAAGAATATAATCTCAG
CAAGGCTGAGAACCACTTAAAACAGATAGAGAAGACAGATGCCAGCAAACACAGAGCAAGGAAGTAGAATTGGCCTCTGT
GAACTGGGAGATTATCTCCATGATGAAAGTTCTAGAAGGAAACAAGAGAAACTTTAATGGTATCTATGAAAAACGTATGG
AGTGCAATTGCCAGTACCAAAACATCCAAGGCCTTTATGATAGCCTTACGCTGAGGAATTTCACCATGGCTAGCCGAGAA
GGCTCCCTGGAACCAGGTGTGATCCCACAGTCTGGAGTCTTTGGCTTCCCACCAGGGAAGAGGTCAAAGTTTTCTTTGGA
CCGTACACCAGTTGGAAATCAAGGTGGCGGAGATGAAGGTGTTCAGTTCGGACCATTTTTTGTGTGTTCTCCCACAGCAC
CCGAACCCGTTAACAACTTCTTTAGTTTTGCGTCTCAAAGGCATGAAACAGAGCAGCGAGTCTGCAGCAGGGCCTTAAAG

Alignment

ORF - retro_rnor_842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.6 %
• Parental protein coverage: 67.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDISSRALAFWTYQVHQERLYQEYNFSKAENHLKQMEKIYT-QQIQSKDVELTSMKGEVTSMKKVLEEYK
          LDISSRALAFWTYQVHQERLYQEYN.SKAENHLKQ.EK....QQ.QSK.VEL.S...E..SM.KVLE..K
Retrocopy LDISSRALAFWTYQVHQERLYQEYNLSKAENHLKQIEKTDA<QQTQSKEVELASVNWEIISMMKVLEGNK

Parental  KKFSDISEKLMERNRQYQKLQGLYDSLRLRNITIASQEGSLEPAMIPQSGVFGFPSGNSSKFSLDHTPAG
          ..F..I.EK.ME.N.QYQ..QGLYDSL.LRN.T.AS.EGSLEP..IPQSGVFGFP.G..SKFSLD.TP.G
Retrocopy RNFNGIYEKRMECNCQYQNIQGLYDSLTLRNFTMASREGSLEPGVIPQSGVFGFPPGKRSKFSLDRTPVG

Parental  NQGGGDEDVQFRPFFVCSPTAPEPVNNFFSFASQSHEAEQQVCSRAFK
          NQGGGDE.VQF.PFFVCSPTAPEPVNNFFSFASQ.HE.EQ.VCSRA.K
Retrocopy NQGGGDEGVQFGPFFVCSPTAPEPVNNFFSFASQRHETEQRVCSRALK

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	0.14 RPM
SRP017611_kidney	0.00 RPM	0.49 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_842 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_842 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009967	2 retrocopies	retro_cjac_3244, retro_cjac_4197,
Homo sapiens	ENSG00000100814	1 retrocopy	retro_hsap_4877,
Gorilla gorilla	ENSGGOG00000004586	1 retrocopy	retro_ggor_3046,
Microcebus murinus	ENSMICG00000000893	2 retrocopies	retro_mmur_1264, retro_mmur_1551,
Macaca mulatta	ENSMMUG00000016251	2 retrocopies	retro_mmul_2617, retro_mmul_371,
Nomascus leucogenys	ENSNLEG00000010636	1 retrocopy	retro_nleu_2556,
Pan troglodytes	ENSPTRG00000006088	1 retrocopy	retro_ptro_3249,
Rattus norvegicus	ENSRNOG00000026056	1 retrocopy	retro_rnor_842 ,
Ictidomys tridecemlineatus	ENSSTOG00000004394	1 retrocopy	retro_itri_1590,