RetrogeneDB ID: retro_rnor_2465

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:72871339..72871812(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gltp
• Ensembl ID: ENSRNOG00000001192
• Aliases: Gltp, RGD1564442
• Description: Glycolipid transfer protein [Source:UniProtKB/Swiss-Prot;Acc:B0BNM9]

Sequence

>retro_rnor_2465
GCAAGCCAAGTGAGTAAGAGGAGAGTGGCAGACCGGCAGACAGACACGGGGCCCTTCCTGGAGGCGGTGGCCCACCTGCC
ATCCTGCAATTGCCTTGGGTCCCCAGTGTTCACGCCCATCAAGACAGACATAAGCGATAACATTACCAAAATCAAAGCAG
CCTATGACACTGACCCAGCCAAGTTCAAGACCCTGTAGAACATCCTGGAGGTGGAAAAGGGGATGTACGGAGTGGACTGC
CAAGTTGGGGCCACGCTGGCACTGCTGTGACTGAAAGGGGCCTGCGCTTCATCCAGGTGTTCCTGCAGAGCATCTGCGAT
GAGGAGCGGGATAAGAACCACCCCAACCTCATGTGAGTAACCGCCAACAAGGCCTCTGAGGTGGCCCTTAAGAAGTACCA
TGGCCGGCTGGTGCAGACCTTCAAGGCCTCACTGTATGCAGCACCATACAAGTCCGACTTCCTAAAGGCTCTC

Alignment

ORF - retro_rnor_2465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.4 %
• Parental protein coverage: 77.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEHLLKPLPADRQIETGPFLEAVAHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTDPAKFKTLQNIL
          A....K...ADRQ..TGPFLEAVAHLP....CLGSPVFTPIK.DIS.NITKIKA.YDTDPAKFKTL.NIL
Retrocopy ASQVSKRRVADRQTDTGPFLEAVAHLPSC-NCLGSPVFTPIKTDISDNITKIKAAYDTDPAKFKTL*NIL

Parental  EVEKGMYGAEWPKVGATLALLWLK-RGLRFIQVFLQSICDGERDENHPNLIRVNANKAYEMALKKYHGWL
          EVEKGMYG.....VGATLALL.LK.RGLRFIQVFLQSICD.ERD.NHPNL..V.ANKA.E.ALKKYHG.L
Retrocopy EVEKGMYGVDC-QVGATLALL*LK<RGLRFIQVFLQSICDEERDKNHPNLM*VTANKASEVALKKYHGRL

Parental  VQKIFKAALYAAPYKSDFLKAL
          VQ..FKA.LYAAPYKSDFLKAL
Retrocopy VQ-TFKASLYAAPYKSDFLKAL

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	30.12 RPM
SRP017611_kidney	0.00 RPM	13.61 RPM
SRP017611_liver	0.00 RPM	3.43 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2465 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2465 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2465 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012545	5 retrocopies	retro_mluc_1056, retro_mluc_1902, retro_mluc_2135, retro_mluc_2397, retro_mluc_658,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28,
Pan troglodytes	ENSPTRG00000005431	1 retrocopy	retro_ptro_41,
Rattus norvegicus	ENSRNOG00000001192	1 retrocopy	retro_rnor_2465 ,