RetrogeneDB ID: retro_rnor_1155

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:83688318..83688737(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Akip1
• Ensembl ID: ENSRNOG00000013744
• Aliases: Akip1, RGD1306959
• Description: proline-rich protein BCA3 [Source:RefSeq peptide;Acc:NP_001101967]

Sequence

>retro_rnor_1155
TGTCTAGTGGCCGCAGCGTGGAAGAGGTGGACCGGTGGTTGCTACAGTGGCCTACTAGTGTAGGGAGGGAAGTACTAGAT
CACACAAAGAGGAGGGTAGTGGACTGGCACTCTCCAGAGTGATCCAGAGGCAGTGTGGGGGTCCTTTACTGCCAGGGCCC
CTACCGGAATGATGGTCAGTCCCAGATCCCCAGTGCCCCCTAGGAGAGAAAGAAGACAGGCACCCAACCCTTAGTTCTTC
CTTCAGAACAATGGCTGAATTCATGGACTATACTTCAAGTCAGTGTGGGAAATACTACTCGTCTATACCAGAGGGAGGGG
CGGGGGGCAACCCATGTCTACCTTTATCACAGAAGGAAGCCTCCAGAAGTGCACGTGTACTCAGACACAGGGCATAGTGA
AGAGCAAAGAAACTGCAGA

Alignment

ORF - retro_rnor_1155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.93 %
• Parental protein coverage: 61.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CLAAAA-LNAVDRRSLQRSARLGREVLERAKRRAVDWHSPERSRGCVGVLYGQDPYQ-ERWSVPGPQSLL
          CL.AAA....VDR..LQ.....GREVL...KRR.VDWHSPE.SRG.VGVLY.Q.PY..E.WSVP.PQ..L
Retrocopy CLVAAA<VEEVDRWLLQWPTSVGREVLDHTKRRVVDWHSPE*SRGSVGVLYCQGPYR<E*WSVPDPQCPL

Parental  GEREERRPTLSTSFRTMAEFMDYTSSQCGKYYLSTPE-EG-GATHVYRYHRRKPAEVHVCSDSGHREAQV
          GE.E.R.PTLS.SFRTMAEFMDYTSSQCGKYY.S.PE.EG.GATHVY.YHRRKP.EVHV.SD.GH.E.Q.
Retrocopy GEKEDRHPTLSSSFRTMAEFMDYTSSQCGKYYSSIPE>EGRGATHVYLYHRRKPPEVHVYSDTGHSEEQR

Parental  RAR
          ..R
Retrocopy NCR

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	2.66 RPM
SRP017611_kidney	0.00 RPM	3.98 RPM
SRP017611_liver	0.00 RPM	2.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1155 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1155 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1155 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006233	1 retrocopy	retro_chof_1889,
Pteropus vampyrus	ENSPVAG00000000411	1 retrocopy	retro_pvam_1460,
Rattus norvegicus	ENSRNOG00000013744	1 retrocopy	retro_rnor_1155 ,