RetrogeneDB ID: retro_rnor_68

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:85031734..85033111(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000038211
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Chn1
• Ensembl ID: ENSRNOG00000017939
• Aliases: None
• Description: N-chimaerin [Source:UniProtKB/Swiss-Prot;Acc:P30337]

Sequence

>retro_rnor_68
ATGGCCCTGACCCTGTTCGATACAGATGAATATAGACCTCCTGTTCGGAAATCTTACTTATACCAGCTGCAGCAGGAAGC
CCCTCACCCTCGAAGGATCACCTGCACTTGCAAGGTAGAAAACAGACCAAAGTATTATGGAAGAGAGTTTCATGGTATGA
TCTCTAGAGAAGAAACTGACCAGCTCCTGAGTGTGGCTGAGGGGAGCTACCTCATCCGTGAGAGCCAGCAGCAGCCTGGA
ATGTACACTTTGGCTTTAAGATTTGAAAGTCAGACTAGAAACTTCAGGCTGTACTATGATGGAAAGCACTTTGTTGGGGA
CAAACGCTTTGAGTCCATCCACGATCTGGTGACTGATGGCTTGAATACTCTCTATATTGAAACCAAGACAGCAGAATACA
TTGCCAAGATGACGATAAACCCAATTTATGAGCACATAGGATACACAACCTTACACAGAGGGCCAGCATACAAACAGCAC
ATGGCAGTCCTGAAAAAGACACACGATAAGAAAAAGGCTACAGGCCAGAATGAGGTGTCAGACAAAAGGTTGACATCACT
TGTTAGAAGAGCAACTCTGAAAGAAAATGAACAAATTCCAAAATATGAGAAGGTTCACAATTTCAAGGTTCGTATGTTCC
GAGGGTCACACTGGTGTGAATATTGTGCCAACTTCATGTGGGGCCTCATTGCTCAGAGAGTGAAATGTGCAGATTGTGGG
TTGAATGTTCACAAGCAGTGTTCCAAGATGGTCGCCAATGACTGTAAGCCAGACCTGAAGCACGTGAAGAAGGTGTACAG
CTGTGACCTAACAACGCTCGTGAAAGCTCACATCACCAAGCGGCCAATGGTGGTAGACATGTGCATCAGGGAGATTGAGT
CCAGAGGTCTGAAATCTGAAGGACTCTACCGAGTGTCGGGATTTAGTGACCTAATTGAAGACGTCAAGATGGCTTTTGAT
AGAGACGGTGAAAAGGCAGATATTTCTGTGAACGTGTATGAGGACATCAACATTATCACTGGGGCACTTAAACTGTACTT
CAAGGACCTGCCAATTCCCCTCATCACCTACGATGCCTACCCCAAGTTCATAGAGTCCGTCAAAATTATGGACCCTGATG
AGCAATTGGAGACCCTTCATGAAGCACTCAGATCTCTGCCGCCGGCCCACTGCGAGACGCTTCGGTACCTCATGGCACAC
CTCAAGAGAGTGACCCTTCACGAGAAGGAGAATCTGATGAGTGCAGAGAACCTTGGGATTGTGTTTGGTCCAACCCTCAT
GAGATCACCAGAGTTAGACCCCATGGCCGCCCTGACTGACATACGCTATCAGAGACTGGTGGTGGAGCTGCTTATCAAAA
ATGAAGACATTTTTAAT

Alignment

ORF - retro_rnor_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.64 %
• Parental protein coverage: 82.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLTSLVRRATLKENEQIPKYEKVHNFKVHTFRGPHWCEYCANFMWGLIAQGVKCADCGLNVHKQCSKMVP
          .LTSLVRRATLKENEQIPKYEKVHNFKV..FRG.HWCEYCANFMWGLIAQ.VKCADCGLNVHKQCSKMV.
Retrocopy RLTSLVRRATLKENEQIPKYEKVHNFKVRMFRGSHWCEYCANFMWGLIAQRVKCADCGLNVHKQCSKMVA

Parental  NDCKPDLKHVKKVYSCDLTTLVKAHITKRPMVVDMCIREIESRGLNSEGLYRVSGFSDLIEDVKMAFDRD
          NDCKPDLKHVKKVYSCDLTTLVKAHITKRPMVVDMCIREIESRGL.SEGLYRVSGFSDLIEDVKMAFDRD
Retrocopy NDCKPDLKHVKKVYSCDLTTLVKAHITKRPMVVDMCIREIESRGLKSEGLYRVSGFSDLIEDVKMAFDRD

Parental  GEKADISVNMYEDINIITGALKLYFRDLPIPLITYDAYPKFIESAKIVDPDEQLETLHEALRSLPPAHCE
          GEKADISVN.YEDINIITGALKLYF.DLPIPLITYDAYPKFIES.KI.DPDEQLETLHEALRSLPPAHCE
Retrocopy GEKADISVNVYEDINIITGALKLYFKDLPIPLITYDAYPKFIESVKIMDPDEQLETLHEALRSLPPAHCE

Parental  TLRYLMAHLKRVTLHEKENLMSAENLGIVFGPTLMRSPELDPMAALNDIRYQRLVVELLIKNEDI
          TLRYLMAHLKRVTLHEKENLMSAENLGIVFGPTLMRSPELDPMAAL.DIRYQRLVVELLIKNEDI
Retrocopy TLRYLMAHLKRVTLHEKENLMSAENLGIVFGPTLMRSPELDPMAALTDIRYQRLVVELLIKNEDI

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	1.44 RPM	873.25 RPM
SRP017611_kidney	0.00 RPM	2.23 RPM
SRP017611_liver	0.00 RPM	0.74 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_68 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_68 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_68 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000017939	1 retrocopy	retro_rnor_68 ,