RetrogeneDB ID: retro_rnor_528

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:227541874..227542453(+)
• Located in intron of: ENSRNOG00000020350

Retrocopy information

• Ensembl ID: ENSRNOG00000020409
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: F11r
• Ensembl ID: ENSRNOG00000004414
• Aliases: F11r, Jam1
• Description: Junctional adhesion molecule A [Source:UniProtKB/Swiss-Prot;Acc:Q9JHY1]

Sequence

>retro_rnor_528
ATGGTCTCTAAGGACAGGGGTCAGAACTACGGGGAGGTCAGCATCCACCTCACTGTGCTTGTGCCTCCATCCAAGCCGAC
AGTCAATATCCCCTCCTCTGTCACCATTGGGAACAGGGCAGTGCTGACCTGCTCAGAACATGACGGTTCCCCTCCTTCTG
AGTATTCCTGGTTCAAGGATGGGGTACCTATGCTTATAGCAGACGCCAAGAAAACCTGTGCCTTCATCAATACATCTTCA
TACACCATCGATCCAAAATCAGGGGATCTGGTCTTTGACCCTGTGTCAGCCTTTGATAGTGGCGAATGCTACTGCCAGGC
ACAGAACGGGTATGCGACAGCCATGAGGTCAGAGGCTGTACGCATGGAGGCTGTGGAGCTGAATGTGGCGGGCATCATGG
CAGCTGTCCTGGTAATACTGATTCTCCTTGGACTCTTGATTTTTGGCATCTGGTTTGCCTATAGCCATGGATACTTTGAA
AGAACAAAGAAAGGGACTGCACCGGGTAAGAAGGTGATTTACAGCCAGCCCAGTGCTCGCAGTGAGGGGGAATTCAAACA
GACCTCGTCATTCCTGGTG

Alignment

ORF - retro_rnor_528 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 64.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSEDGGQNYGEVSIHLTVLVPPSKPTVSIPSSVTIGNRAVLTCSEHDGSPPSEYSWFKDGVPMLTADAK
          MVS.D.GQNYGEVSIHLTVLVPPSKPTV.IPSSVTIGNRAVLTCSEHDGSPPSEYSWFKDGVPML.ADAK
Retrocopy MVSKDRGQNYGEVSIHLTVLVPPSKPTVNIPSSVTIGNRAVLTCSEHDGSPPSEYSWFKDGVPMLIADAK

Parental  KTRAFIN-SSYTIDPKSGDLVFDPVSAFDSGEYYCEAQNGYGTAMRSEAVRMEAVELNVGGIVAAVLVTL
          KT.AFIN.SSYTIDPKSGDLVFDPVSAFDSGE.YC.AQNGY.TAMRSEAVRMEAVELNV.GI.AAVLV.L
Retrocopy KTCAFINTSSYTIDPKSGDLVFDPVSAFDSGECYCQAQNGYATAMRSEAVRMEAVELNVAGIMAAVLVIL

Parental  ILLGLLIFGIWFAYSRGYFERTKKGTAPGKKVIYSQPSARSEGEFKQTSSFLV
          ILLGLLIFGIWFAYS.GYFERTKKGTAPGKKVIYSQPSARSEGEFKQTSSFLV
Retrocopy ILLGLLIFGIWFAYSHGYFERTKKGTAPGKKVIYSQPSARSEGEFKQTSSFLV

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	5.97 RPM
SRP017611_kidney	0.28 RPM	109.84 RPM
SRP017611_liver	0.20 RPM	98.37 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_528 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_528 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
Erinaceus europaeus	ENSEEUG00000000928	1 retrocopy	retro_eeur_154,
Echinops telfairi	ENSETEG00000016382	1 retrocopy	retro_etel_955,
Rattus norvegicus	ENSRNOG00000004414	1 retrocopy	retro_rnor_528 ,