RetrogeneDB ID: retro_rnor_1107

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:49057285..49058079(+)
• Located in intron of: ENSRNOG00000015939

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gltscr2
• Ensembl ID: ENSRNOG00000013023
• Aliases: None
• Description: glioma tumor suppressor candidate region gene 2 protein [Source:RefSeq peptide;Acc:NP_997474]

Sequence

>retro_rnor_1107
CTGGAGCAGACCAACAAGAAAGGCACGAGGAAGCCACCCCACCTCCACGTTAAGCCTTGCCAGGTGCCCGCAGTGGAGGT
GATTCCTGGAGGCACCTCCTACAACCCAAGCTTTGAAGATCACCAGGCCTTGCTTTGAAAGGCCCAGGAGGTGGAGCTGC
AGAGTGAGAAAGACACAGGAAAGCCAGAGCAACAGCTGGCCCTGCCCACCATAGAGCAAGCTGCTACCCAGGAGTTCGTG
TTTCGGGAGACGTGTGAGGGCCTGTTCAAAGAGTCTGAGGATGAGGAGGGGCCAGGCTGTGCTGAGCAGCCAGAGGCTGA
TGATGGGGCCACTGAGACCTTACTCACTAGTGCTGCTGGTCCTGAGAAGAGGATAGAGAAGACAGAGGAGCAGCAGCAGC
GGAGGCAGGAGAAGGCTGCTCACAGGCTGCGGGTGCTGAGGAAGCCCAGCTTCAGCACCAAGAACTCTTCAGGCTGCGTG
GGATCAAGGCCCAGGTGGCCCAAAGGCTGGCAGAACTGGCACGCCAGAGGGAGCAGTGCCGCATTCAGCGACTGGTAGAG
GCTGACAAGCCCGAAAGGCTGGGATGGCTCAAGTACCAGGCCCCTGACATTGATGTGCAGCTCAGTTCTGAGCTGTCTGG
CTCACTCAGAATGAAGCAAGAAGGTAACATCCTCTGAGACAGGTTCAAGACCTTCCAGAAGAGATATATGATTGAGCCCC
GGGAACGAGCCAAGCTCAAGCGCAAACACAAAGTGAAGCTGGTGGAGAAGGGGGCCTTCATGAGATTCAGGCTC

Alignment

ORF - retro_rnor_1107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.69 %
• Parental protein coverage: 55.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEQTKKKGVRRPPRLHIKPSQVPAVEVIPAGASYNPTFEDHQALLLEAHEVELQREKEAEKLERQLALPT
          LEQT.KKG.R.PP.LH.KP.QVPAVEVIP.G.SYNP.FEDHQALL..A.EVELQ.EK...K.E.QLALPT
Retrocopy LEQTNKKGTRKPPHLHVKPCQVPAVEVIPGGTSYNPSFEDHQALL*KAQEVELQSEKDTGKPEQQLALPT

Parental  AEQAATQESVFREMCEGLLEESEDEDGPGCAEQPEADDGATETSPTGAAGPEKRMEKKTEQ-QRRREKAA
          .EQAATQE.VFRE.CEGL..ESEDE.GPGCAEQPEADDGATET..T.AAGP....EK..E..QR......
Retrocopy IEQAATQEFVFRETCEGLFKESEDEEGPGCAEQPEADDGATETLLTSAAGP----EKRIEK>QRSSSSGG

Parental  RKLRV-QQAALRAARLQHQELFRLRGIKAQVARRLAELARRKEQRRIRRLAEADKPRRLGRLKYQAPDID
          R.....Q.A....A.LQHQELFRLRGIKAQVA.RLAELAR..EQ.RI.RL.EADKP.RLG.LKYQAPDID
Retrocopy RRRLL>QAAGAEEAQLQHQELFRLRGIKAQVAQRLAELARQREQCRIQRLVEADKPERLGWLKYQAPDID

Parental  VQLSSELSDSLRKLKPEGNILRDRFKSFQKRNMIEPRERAKFKRKYKVKLVEKRAFREIQL
          VQLSSELS.SLR..K.EGNIL.DRFK.FQKR.MIEPRERAK.KRK.KVKLVEK.AF....L
Retrocopy VQLSSELSGSLR-MKQEGNIL*DRFKTFQKRYMIEPRERAKLKRKHKVKLVEKGAFMRFRL

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	54.57 RPM
SRP017611_kidney	0.00 RPM	70.27 RPM
SRP017611_liver	0.07 RPM	30.59 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1107 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1107 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105373	1 retrocopy	retro_hsap_1528,
Macropus eugenii	ENSMEUG00000002525	2 retrocopies	retro_meug_1136, retro_meug_1713,
Nomascus leucogenys	ENSNLEG00000003143	1 retrocopy	retro_nleu_1937,
Pongo abelii	ENSPPYG00000010181	3 retrocopies	retro_pabe_1270, retro_pabe_653, retro_pabe_662,
Pan troglodytes	ENSPTRG00000011215	1 retrocopy	retro_ptro_1035,
Rattus norvegicus	ENSRNOG00000013023	1 retrocopy	retro_rnor_1107 ,