RetrogeneDB ID: retro_rnor_566

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:18721968..18723219(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000049777
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Blmh
• Ensembl ID: ENSRNOG00000003563
• Aliases: None
• Description: Bleomycin hydrolase [Source:UniProtKB/Swiss-Prot;Acc:P70645]

Sequence

>retro_rnor_566
ATGAACAACGCAGGACTAAATTCGGAGAAGGTATCTGCTTTGATCCAGAAACTAAATTCTGACCCTCAGTTCGTACTTGC
CCAGAATGTCGGGACCACCCACGATCTGCTGGACATATGTCTGAGGAGGGCCACGGTCCAGGGTGCTCAGCATGTGTTTC
AACACGTTGTGCCTCAGGAAGGCAAGCCAGTCACCAACCAGAAGAGCTCTGGACGATGCTGGATCTTTTCTTGTTTGAAT
GTTATGAGACTTCCATTCATGAAAAAATTTAACATTGAAGAATTTGAGTTTAGTCAATCTTACCTGTTTTTTTGGGACAA
GGTTGAACGCTGTTATTTCTTCTTGAATGCTTTTGTGGACACAGCTCAGAAAAAGGAGCCTGAAGATGGGAGACTGGTGC
AGTATTTGCTTATGAACCCTACAAATGATGGTGGACAGTGGGATATGCTTGTCAATATTGTTGAAAAATACGGTGTTGTT
CCTAAGAAATGCTTTCCCGAATCGCATACGACAGAGGCTACCAGAAGAATGAATGATATTCTGAATCACAAGATGAGAGA
ATTCTGTATACGGCTTCGGAACCTGGTACACAGTGGAGCCACCAAAGGGGAGATCTCATCTACACAAGATGCCATGATGG
AGGAGATATTCAGAGTGGTGTGCATCTGTTTGGGCAACCCACCAGAGACCTTCACCTGGGAGTACCGAGACAAAGATAAA
AATTACCACAAGATTGGCCCCATAACACCCTTGCAGTTTTACAAGGAGCACGTGAAGCCGCTCTTCAATATGGAAGATAA
GATTTGTTTTGTGAATGACCCACGGCCCCAGCACAAGTACAATAAATTGTACACAGTAGACTACTTGAGCAATATGGTTG
GAGGGAGAAAAACGCTGTATAACAACCAGCCCATTGACTTCTTGAAAAAGATGGTTGCTGCCTCCATCAAAGATGGAGAG
GCTGTGTGGTTTGGCTGTGATGTTGGAAAACACTTCAATGGCAAGCTGGGCCTCAGTGACATGAATGTCTATGACCATGA
GTTAGTGTTCGGTGTCTCCTTGAAGAACATGAATAAAGCTGAGAGGTTGGCCTTTGGTGAGTCACTCATGACCCACGCCA
TGACCTTCACTGCTGTCTCAGAGAAGGATAATCAGGAAGGTACTTTTGTGAAATGGAGAGTAGAGAATTCATGGGGTGAA
GACCACGGCCACAAAGGCTACCTGTGCATGACCGATGAGTGGTTCTCGGAG

Alignment

ORF - retro_rnor_566 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.56 %
• Parental protein coverage: 91.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNNAGLNSEKVAALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQGAQHVFQHVVPQEGKPVTNQKSS
          MNNAGLNSEKV.ALIQKLNSDPQFVLAQNVGTTHDLLDICL.RATVQGAQHVFQHVVPQEGKPVTNQKSS
Retrocopy MNNAGLNSEKVSALIQKLNSDPQFVLAQNVGTTHDLLDICLRRATVQGAQHVFQHVVPQEGKPVTNQKSS

Parental  GRCWIFSCLNVMRLPFMKKFNIEEFEFSQSYLFFWDKVERCYFFLNAFVDTAQKKEPEDGRLVQYLLMNP
          GRCWIFSCLNVMRLPFMKKFNIEEFEFSQSYLFFWDKVERCYFFLNAFVDTAQKKEPEDGRLVQYLLMNP
Retrocopy GRCWIFSCLNVMRLPFMKKFNIEEFEFSQSYLFFWDKVERCYFFLNAFVDTAQKKEPEDGRLVQYLLMNP

Parental  TNDGGQWDMLVNIVEKYGVVPKKCFPESHTTEATRRMNDILNHKMREFCIRLRNLVHSGATKGEISSTQD
          TNDGGQWDMLVNIVEKYGVVPKKCFPESHTTEATRRMNDILNHKMREFCIRLRNLVHSGATKGEISSTQD
Retrocopy TNDGGQWDMLVNIVEKYGVVPKKCFPESHTTEATRRMNDILNHKMREFCIRLRNLVHSGATKGEISSTQD

Parental  AMMEEIFRVVCICLGNPPETFTWEYRDKDKNYHKVGPITPLQFYKEHVKPLFNMEDKICFVNDPRPQHKY
          AMMEEIFRVVCICLGNPPETFTWEYRDKDKNYHK.GPITPLQFYKEHVKPLFNMEDKICFVNDPRPQHKY
Retrocopy AMMEEIFRVVCICLGNPPETFTWEYRDKDKNYHKIGPITPLQFYKEHVKPLFNMEDKICFVNDPRPQHKY

Parental  NKLYTVDYLSNMVGGRKTLYNNQPIDFLKKMVAASIRDGEAVWFGCDVGKHFNGKLGLSDMNVYDHELVF
          NKLYTVDYLSNMVGGRKTLYNNQPIDFLKKMVAASI.DGEAVWFGCDVGKHFNGKLGLSDMNVYDHELVF
Retrocopy NKLYTVDYLSNMVGGRKTLYNNQPIDFLKKMVAASIKDGEAVWFGCDVGKHFNGKLGLSDMNVYDHELVF

Parental  GVSLKNMNKAERLAFGESLMTHAMTFTAVSEKDDQEGAFVKWRVENSWGEDHGHKGYLCMTDEWFSE
          GVSLKNMNKAERLAFGESLMTHAMTFTAVSEKD.QEG.FVKWRVENSWGEDHGHKGYLCMTDEWFSE
Retrocopy GVSLKNMNKAERLAFGESLMTHAMTFTAVSEKDNQEGTFVKWRVENSWGEDHGHKGYLCMTDEWFSE

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	30.56 RPM
SRP017611_kidney	0.07 RPM	41.45 RPM
SRP017611_liver	0.13 RPM	16.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_566 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_566 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021370	1 retrocopy	retro_btau_1510,
Callithrix jacchus	ENSCJAG00000013781	1 retrocopy	retro_cjac_2998,
Cavia porcellus	ENSCPOG00000005048	1 retrocopy	retro_cpor_896,
Macropus eugenii	ENSMEUG00000008938	1 retrocopy	retro_meug_2120,
Rattus norvegicus	ENSRNOG00000003563	1 retrocopy	retro_rnor_566 ,
Tursiops truncatus	ENSTTRG00000016341	1 retrocopy	retro_ttru_1915,
Vicugna pacos	ENSVPAG00000003571	1 retrocopy	retro_vpac_74,