RetrogeneDB ID: retro_rnor_2476

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:102505121..102505858(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gcm1
• Ensembl ID: ENSRNOG00000007932
• Aliases: Gcm1, Gcma
• Description: Chorion-specific transcription factor GCMa [Source:UniProtKB/Swiss-Prot;Acc:Q9Z288]

Sequence

>retro_rnor_2476
ATGGAACTGGACAACTGTGATCCTGAAGACAAGAGATACTGAGCTGGGATATTAACGACATGAAGCTGCCTCAGAATGTG
AAGAAGACTGACTGGTTCCAGGAGTGGCCAGACTCCTATGTGAAACACAGCTACAGCTCAGACGACAGGAGCGCACAGCA
CCATCTGAGCAGCTGGGCCATGCGCAACAGCAACAACCACAACTCCCAGATCCTCAAGAAGTCGTGCCTGGGGGTAGTGG
TGTGCACCAGGAACTGTTCCACGGAGAAAGGCCGCAAGATTTATCTGAGACCCACCATCTGTGACAAAGCCAGGCAGAAG
CAGCAGAGGAAAAGCTGTCCCAACTGCAATGGACCCCTGAAACTAATTCCCTGCAGAGGCCACGGCGGCTTCCCGATCAC
CAACTTCTAGAGGCATGACAGACGCTTCATCTTTTTCTAGTCCAAAGGAGAGCACGATCATCCCAGGCCGGAGACCAATC
TAGAAACAGAGGCAAGAAGAGCAGTGAAGAAAGTGCACATGGCCTCTGCCTCCAGCTCCTTACGGATGAAGGGGAGACCA
GAAATGAAGGGTCTTCCAGGTGAAATCCCGAGTCAGGGAAGTTTACCTTTAACTGGGTCATTCCAGGAAGGCGTCCAACT
GCCCAGCGGTTATAGCACACCTTTAATAGCTAACGCTCCCCAGCAGAACTCCCTGAATGATTGCCTGTCCTTCCCCAAGA
GTTATGACTTGGGGGGA

Alignment

ORF - retro_rnor_2476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 56.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MELDDFDPEDK-EILSWDINDMKLPQNVKKTDWFQEWPDSYVKHIYSSDDRSAQRHLSSWAMRNTNNHNS
          MELD..DPEDK.EILSWDINDMKLPQNVKKTDWFQEWPDSYVKH.YSSDDRSAQ.HLSSWAMRN.NNHNS
Retrocopy MELDNCDPEDK<EILSWDINDMKLPQNVKKTDWFQEWPDSYVKHSYSSDDRSAQHHLSSWAMRNSNNHNS

Parental  RILKKSCLGVVVCSRDCSTEEGRKIYLRPAICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFPVTNFWRH
          .ILKKSCLGVVVC.R.CSTE.GRKIYLRP.ICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFP.TNF.RH
Retrocopy QILKKSCLGVVVCTRNCSTEKGRKIYLRPTICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFPITNF*RH

Parental  DGRFIFFQSKGEHDHPRPETKLEAEARRAMKKVHMASASSSLRMKGRPEMKGLPGEIPSQGSLPLTWSFQ
          D.RFIFF.SKGEHDHPRPET.LE.EARRA.KKVHMASASSSLRMKGRPEMKGLPGEIPSQGSLPLT.SFQ
Retrocopy DRRFIFF*SKGEHDHPRPETNLETEARRAVKKVHMASASSSLRMKGRPEMKGLPGEIPSQGSLPLTGSFQ

Parental  EGVQLPSGYSTPLIANAPQQNSLNDCLSFPKSYDLGG
          EGVQLPSGYSTPLIANAPQQNSLNDCLSFPKSYDLGG
Retrocopy EGVQLPSGYSTPLIANAPQQNSLNDCLSFPKSYDLGG

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	1.65 RPM	0.29 RPM
SRP017611_kidney	0.00 RPM	7.68 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2476 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2476 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002273	1 retrocopy	retro_cfam_466,
Rattus norvegicus	ENSRNOG00000007932	1 retrocopy	retro_rnor_2476 ,
Ictidomys tridecemlineatus	ENSSTOG00000014763	1 retrocopy	retro_itri_77,