RetrogeneDB ID: retro_rnor_80

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:260515288..260516839(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000018925
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000025353
• Aliases: Ears2, RGD1307904
• Description: None

Sequence

>retro_rnor_80
GTAATGCTGGCCGGGCCTCACGTGGGGGCCCTCGGGCACCGCGTGGGTCGGCGCGAGGCCAGTCTGGGCCCAGATCCCGG
GGTCACGGTGCGAGTGCGCTTCGCTCCCAGCCCCACAGGCTTCTTACACCTGGGTGGCCTCCGTACTGCCCTCTACAACT
ACATCTTTGCCAAGAAGCACCAAGAGAGCTTCATTCTGAGGCTGGAGGACACTGATCAGAGCCGCCTGGTACCGGGGGCA
GCAGAAAACATTGAGGACATGCTGGAGTGGGCAGGCATCCCACCTGATGAAAGTCCCCGCCGGGGTGGTCCTGCAGGGCC
CTACTATCAGTCACAGCGGCTAGCTCTGTATGCCCAGGCCACAGAAGCATTGCTGAAATCTGGAGCTGCCTATCCCTGTT
TCTGTTCACCACAGCGGCTGGAGCTCCTGAAGAAGGAAGCACTGAGGAGCCGTCAGACACCTCGGTATGACAATCGATGC
CGGAACCTGAGCCAGGCACAGGTGGCCCAGAAGCTGGCCACAGACCCCAAGCCTGCTATCCGCTTTCGCCTAGAGGAAGC
AGTACCAGCCTTCCAAGACCTGGTATATGGCTGGACTCAGCATGAAGTGGCCAGTGTGGAGGGGGACCCAGTTATCCTGA
AAAGTGATGGCTTTCCTACCTACCACCTAGCCTGTGTGGTAGATGACCACCACATGAGCATCAGCCATGTACTTCGGGGC
TCTGAGTGGTTGGTCTCTACATCCAAGCACTTGCTCCTCTACCAGGCCCTGGGTTGGCAGCCACCTCAATTTGCTCATCT
GCCCCTGCTCCTCAACAGGGATGGTAGCAAGCTGTCTAAGAGGCAAGGGGACATTTTCCTGGAACATTTCGCTGCCACCG
GTTTTCTTCCAGAAGCCTTGCTTGACATCATCACCAACTGTGGCTCGGGGTTTGCAGAGAACCAAATGGGCAGGACCCTG
CCGGAGCTGATTACACAGTTTGACCTGACTCGGATCACCTGCCACTCAGCCCTGCTGGACCTAGAGAAGCTCCCAGAATT
CAACAGGCTGCACCTCCGCCGGCTGGTGAGCAGTGAGACCCAGAGGCCCCATTTGGTGGAGAAGTTGCAGGGCCTGGTGA
AGGAGGCATTTGGGAGCGAACTGCAAGACAGGGATGTTCTGGACCCAGCATATATGGAGAGGATCCTCCTGCTGCGACAG
GGTCACATCAGCCGTCTGCAGGATCTGGTCTCCCCAGTGTACTCCTACTTATGGACCCGCCCTGCTGTCCATCGAGCAGA
GCTGGGCGCCAGCTCGGAAAAGTTGGATGTGATTGCCAAACACTTGCTGGGGCTTTTAGAAAGACCTGGTTTAAGCCTAA
CTCAGGATGTGGTGAACAGAGAACTGAAGAAGCTGTCAGAAGGCCTGGAAGGCACCAAGCATAGCAGCGTGATGAAGCTC
CTCCGGATGGCCCTCAGTGGACAGCTGCAAGGACCCCCTGTGGCTGAGATGATGGTGTCCTTGGGCCCAGAGGAAGTACG
GGAACGAATCCAGAAGGTGCTTTCTAGCTAG

Alignment

ORF - retro_rnor_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIPPDESPRQGGPAGPYYQSQRLALYAQATEALLKSGAAYPCFCSPQRLELLKKEALRSRQTPRYDNRCR
          GIPPDESPR.GGPAGPYYQSQRLALYAQATEALLKSGAAYPCFCSPQRLELLKKEALRSRQTPRYDNRCR
Retrocopy GIPPDESPRRGGPAGPYYQSQRLALYAQATEALLKSGAAYPCFCSPQRLELLKKEALRSRQTPRYDNRCR

Parental  NLSQAQVAQKLATDPKPAIRFRLEEAVPAFQDLVYGWTQHEVASVEGDPVILKSDGFPTYHLACVVDDHH
          NLSQAQVAQKLATDPKPAIRFRLEEAVPAFQDLVYGWTQHEVASVEGDPVILKSDGFPTYHLACVVDDHH
Retrocopy NLSQAQVAQKLATDPKPAIRFRLEEAVPAFQDLVYGWTQHEVASVEGDPVILKSDGFPTYHLACVVDDHH

Parental  MSISHVLRGSEWLVSTSKHLLLYQALGWQPPQFAHLPLLLNRDGSKLSKRQGDIFLEHFAATGFLPEALL
          MSISHVLRGSEWLVSTSKHLLLYQALGWQPPQFAHLPLLLNRDGSKLSKRQGDIFLEHFAATGFLPEALL
Retrocopy MSISHVLRGSEWLVSTSKHLLLYQALGWQPPQFAHLPLLLNRDGSKLSKRQGDIFLEHFAATGFLPEALL

Parental  DIITNCGSGFAENQMGRTLPELITQFDLTRITCHSALLDLEKLPEFNRLHLRRLVSSETQRPHLVEKLQG
          DIITNCGSGFAENQMGRTLPELITQFDLTRITCHSALLDLEKLPEFNRLHLRRLVSSETQRPHLVEKLQG
Retrocopy DIITNCGSGFAENQMGRTLPELITQFDLTRITCHSALLDLEKLPEFNRLHLRRLVSSETQRPHLVEKLQG

Parental  LVKEAFGSELQDRDVLDPAYMERILLLRQGHISRLQDLVSPVYSYLWTRPAVHRAELGASSEKLDVIAKH
          LVKEAFGSELQDRDVLDPAYMERILLLRQGHISRLQDLVSPVYSYLWTRPAVHRAELGASSEKLDVIAKH
Retrocopy LVKEAFGSELQDRDVLDPAYMERILLLRQGHISRLQDLVSPVYSYLWTRPAVHRAELGASSEKLDVIAKH

Parental  LLGLLERPGLSLTQDVVNRELKKLSEGLEGTKHSSVMKLLRMALSGQLQGPPVAEMMVSLGPEEVRERIQ
          LLGLLERPGLSLTQDVVNRELKKLSEGLEGTKHSSVMKLLRMALSGQLQGPPVAEMMVSLGPEEVRERIQ
Retrocopy LLGLLERPGLSLTQDVVNRELKKLSEGLEGTKHSSVMKLLRMALSGQLQGPPVAEMMVSLGPEEVRERIQ

Parental  KVLSS
          KVLSS
Retrocopy KVLSS

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	0.29 RPM	0.93 RPM
SRP017611_kidney	0.84 RPM	1.05 RPM
SRP017611_liver	0.87 RPM	1.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_80 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_80 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_80 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015505	1 retrocopy	retro_meug_53,
Rattus norvegicus	ENSRNOG00000025353	1 retrocopy	retro_rnor_80 ,