RetrogeneDB ID: retro_rnor_472

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:114761002..114761450(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc137
• Ensembl ID: ENSRNOG00000048712
• Aliases: None
• Description: coiled-coil domain containing 137 [Source:MGI Symbol;Acc:MGI:1914541]

Sequence

>retro_rnor_472
AAGAACCAAGCCACTCTGCAGCCAAAGGTGCAGGCAGCTCCCAAGAAGGAGAAGTCTAAGCCGAAGAAAGCGTTCCAGAA
GCGACGACTTGAAAAGGCCCAGAAGAAAAATGAAGCAAGAGCAGTGGACAGATTGGAGCAGGAGTTGCTAAAAGATACTG
TGAAGTTTGGAGAAGTTGTGCAGCAGCCCCCCGGAGCTGACAGTTTAGCCTAGAAGGAGCACAAGCAGAGACGCACCTGG
GAAGAAATCACTAATACTGAAGATGCTTTCGGGCCCTGGTAGTGTGCCCCCGGCTCCAGCCACCTCACTGGCGCGCCAGT
GGACCCTGGGGGAAGAGCTGAAACGGGCTGTGCAGGCTTACAGAGTCCTGAAGAAGCTGTATGGACAGGAAGTGACACCT
GCATTGCCATCAGGCAGCTCTTCCCAGAGGCAGCTCCAGGCTTGTCTA

Alignment

ORF - retro_rnor_472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 51.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNQATRQPEVQAAPKKEKSERKKAFQKRRLEKAQKKKEARAVDRLEQELLKDTVKFGEVVLQPP-ELTVQ
          KNQAT.QP.VQAAPKKEKS..KKAFQKRRLEKAQKK.EARAVDRLEQELLKDTVKFGEVV.QPP.ELTV.
Retrocopy KNQATLQPKVQAAPKKEKSKPKKAFQKRRLEKAQKKNEARAVDRLEQELLKDTVKFGEVVQQPP>ELTV*

Parental  PRRSTSRDAPGKKSLMLKMLLGPGGVSPAPATSLARQRILGEERERAVQAYRALKKLHRQEVTPAQPPGS
          PRRSTSRDAPGKKSL.LKML.GPG.V.PAPATSLARQ..LGEE..RAVQAYR.LKKL..QEVTPA.P.GS
Retrocopy PRRSTSRDAPGKKSLILKMLSGPGSVPPAPATSLARQWTLGEELKRAVQAYRVLKKLYGQEVTPALPSGS

Parental  SSQRQPQACL
          SSQRQ.QACL
Retrocopy SSQRQLQACL

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	12.94 RPM
SRP017611_kidney	0.00 RPM	10.33 RPM
SRP017611_liver	0.00 RPM	6.25 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_472 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_472 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530, retro_nleu_586,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472 ,