RetrogeneDB ID: retro_rnor_2157

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:90953891..90954481(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sppl3-ps1
• Ensembl ID: ENSRNOG00000001178
• Aliases: None
• Description: None

Sequence

>retro_rnor_2157
GGGCCTCTCAGTGTTGCCAAGTTGCTGTCATTCTCCCTGTTCATCATGCTCGTCCTCATCTGGGTTCTCATTGGATACTG
GCTTCTTATGGATGCTCTGGCCACGGGCCTCAGTGTTTTCATGATTGCCTTTGTCTGCCTGCCAAGCCTCAAGTTTTCCT
GCCTGCTTCTTTCAGGGCTTCTCATCTATGATGTCTTCTGGGTGTTTTTTTTTTTTTTTTCGGTCTACATCTTCAACAGC
AATGTCATGGTGAAAGTGGCCACACAGCCAACTGACAATCCCCTCGATGATCTGTCCTGGAAGTTCCACCTAGGAACCAA
TGTGGAGCGGGATGTTCTTGCCTGTCTTTGCCTGGATAATTGGTCTTCTCAAGGTCCACTGGCAGTCGCTTCTCTGGGTT
GGGCATCGGGGACATTGTGATGCCTGGCCTCCTGTTATGCTTTGTTCTTCTCAATGACAGTTACAAGAAACAAGCCAGTG
GCGACTCCTGTGGGGCCCCTGGTCCCGCTAATATCTCTGGGCACATTCAGAAGGTCTCTTACTTCCACCGCATCCTCATC
CGGTACTTTGTAGGTCTGCTCACAGTGACT

Alignment

ORF - retro_rnor_2157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.27 %
• Parental protein coverage: 51.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRFTAAELLSFSLSVMLVLIWVLTGHWLLMDALAMGLCVAMIAFVRLPSLKVSCLLLSGLLIYDVFWVFF
          G....A.LLSFSL..MLVLIWVL.G.WLLMDALA.GL.V.MIAFV.LPSLK.SCLLLSGLLIYDVFWV..
Retrocopy GPLSVAKLLSFSLFIMLVLIWVLIGYWLLMDALATGLSVFMIAFVCLPSLKFSCLLLSGLLIYDVFWVXX

Parental  S---AYIFNSNVMVKVATQPADNPLDVLSRKLHLGPNVGRDVPR-LSLPGKLVFPSSTGSHFSMLGIGDI
          .....YIFNSNVMVKVATQP.DNPLD.LS.K.HLG.NV.RDV...LSLPG.LVF..STGS.FS.LGIGDI
Retrocopy XXXXVYIFNSNVMVKVATQPTDNPLDDLSWKFHLGTNVERDVLA<LSLPG*LVFSRSTGSRFSGLGIGDI

Parental  VMPGLLLCFVLRYDNYKKQASGDSCGAPGPANISGRMQRVSYFHCTLIGYFVGLLTAT
          VMPGLLLCFVL..D.YKKQASGDSCGAPGPANISG..Q.VSYFH..LI.YFVGLLT.T
Retrocopy VMPGLLLCFVLLNDSYKKQASGDSCGAPGPANISGHIQKVSYFHRILIRYFVGLLTVT

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	34.29 RPM
SRP017611_kidney	0.00 RPM	27.01 RPM
SRP017611_liver	0.00 RPM	11.63 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2157 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2157 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2157 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016589	1 retrocopy	retro_dnov_175,
Homo sapiens	ENSG00000157837	1 retrocopy	retro_hsap_1898,
Gorilla gorilla	ENSGGOG00000016245	1 retrocopy	retro_ggor_1392,
Myotis lucifugus	ENSMLUG00000012754	1 retrocopy	retro_mluc_672,
Macaca mulatta	ENSMMUG00000020650	1 retrocopy	retro_mmul_1359,
Pongo abelii	ENSPPYG00000005041	2 retrocopies	retro_pabe_1578, retro_pabe_1579,
Pan troglodytes	ENSPTRG00000005548	1 retrocopy	retro_ptro_1275,
Rattus norvegicus	ENSRNOG00000001178	1 retrocopy	retro_rnor_2157 ,
Rattus norvegicus	ENSRNOG00000011652	1 retrocopy	retro_rnor_1750,
Sarcophilus harrisii	ENSSHAG00000015326	1 retrocopy	retro_shar_660,