RetrogeneDB ID: retro_rnor_1015

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:83068511..83069597(+)
• Located in intron of: ENSRNOG00000017548

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmem129
• Ensembl ID: ENSRNOG00000017329
• Aliases: Tmem129, RGD1310828
• Description: transmembrane protein 129 [Source:RefSeq peptide;Acc:NP_001119746]

Sequence

>retro_rnor_1015
ATGGACAGCCCTGAGGTGACCTTCACGTTGGCCTACCTGGTCTTCGCAGTGTGCTTCGTGTTCACGCCCAACGAGTTCTA
CTCGGCTGGGCTCACAGTGCAGAATCTGTTGTCGGGCTGGCTGGGCAGCGAGGACGCCGCCTTCGTACCTTACCACCTTC
GCCGCACTTCCGCCACACTACTATGTCACTCACTGCTGCCGTTAGGCTACTACATGGGCATGTGCTTTGCAGCCTCAGAA
AAGCAGCTCTACTCCCCAGGTCAGGCCCCAGAAGCCTGGCAACTCTTCCTTCTCCTGGCTGTGACCCTTCCCCTTCTCTC
CTGTACCCTGATCTACTACTGGTCCTGGGATAGGTGGACCCGACACCCACTGGCCCAAACCCTGGCCCTCTATGCCCTTC
CACAGTCTGGTTGGCAGGCTGTCGCTTCTTCCATCAACACAGAGTTCCGACGGATTGACAAGTTTGCTACAGGGGCACCT
GGTGCCCGAGTGATTGTGACAGACACATGGGTAATGAAGGTGACCACATACCGTGTGCATGTGGCTCAGCAACAGGATGT
TCACTTGACTGTGACAGAGTCACGGCAGCATGATCTCTCGCCAGACTCAAACCTACCTGTGCAGCTTCTTACTATACGTG
TGGCAAGCACCAGCCCTGGCACACAGCCCTTTGATATTCGGCTGAATTCATCAGAATATGGCGAACTATGTGAGAAGCTC
CACGCCCCAATCCGAAGTGCAGCCAATGTGGTCATCCGCCAGAGCCTGGGGGACCTCTTCCTAGAAACATTTGCTTCCCA
TGTGGAGGTCAACCCAGCCTATTCAGTACCCAGCAACCAGGAGCTGGAGCCCTGTATAGGCTGCATGCAAACACGGGCCA
GCGTGAAGTTGGTGAAGACCTGTCAGGAGCCAGCGGTCGGCGAGTGCCAGCAGTGTTACTGCCGACCCATGTGGTGTCTC
ACTTGCATGGGCAAGTGGTTTGCCAGCCGCCAGGATCCCCAGCGCCCTGACACTTGGCTAGCCAGCCGTGTGCCCTGCCC
CACTTGCCGTGCCCGCTTCTGCATCCTGGATGTGTGCTGTGTACGC

Alignment

ORF - retro_rnor_1015 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSPEVTFTLAYLVFAVCFVFTPNEFYSAGLTVQNLLSGWLGSEDAAFVPYHLRRTSATLLCHSLLPLGY
          MDSPEVTFTLAYLVFAVCFVFTPNEFYSAGLTVQNLLSGWLGSEDAAFVPYHLRRTSATLLCHSLLPLGY
Retrocopy MDSPEVTFTLAYLVFAVCFVFTPNEFYSAGLTVQNLLSGWLGSEDAAFVPYHLRRTSATLLCHSLLPLGY

Parental  YMGMCFAASEKQLYSPGQAPEAWQLFLLLAVTLPLVSCTLIYYWSWDRWARHPLAQTLALYALPQSGWQA
          YMGMCFAASEKQLYSPGQAPEAWQLFLLLAVTLPL.SCTLIYYWSWDRW.RHPLAQTLALYALPQSGWQA
Retrocopy YMGMCFAASEKQLYSPGQAPEAWQLFLLLAVTLPLLSCTLIYYWSWDRWTRHPLAQTLALYALPQSGWQA

Parental  VASSINTEFRRIDKFATGAPGARVIVTDTWVMKVTTYRVHVAQQQDVHLTVTESRQHDLSPDSNLPVQLL
          VASSINTEFRRIDKFATGAPGARVIVTDTWVMKVTTYRVHVAQQQDVHLTVTESRQHDLSPDSNLPVQLL
Retrocopy VASSINTEFRRIDKFATGAPGARVIVTDTWVMKVTTYRVHVAQQQDVHLTVTESRQHDLSPDSNLPVQLL

Parental  TIHVASTSPGAQPFDIRLNSSEYGELCEKLRAPIRSAANVVIRQSLGDLFLETFASLVEVNPAYSAPSNQ
          TI.VASTSPG.QPFDIRLNSSEYGELCEKL.APIRSAANVVIRQSLGDLFLETFAS.VEVNPAYS.PSNQ
Retrocopy TIRVASTSPGTQPFDIRLNSSEYGELCEKLHAPIRSAANVVIRQSLGDLFLETFASHVEVNPAYSVPSNQ

Parental  ELEACIGCMQTRASVKLVKTCQEPAVGECQQCYCRPMWCLTCMGKWFASRQDPQRPDTWLASRVPCPTCR
          ELE.CIGCMQTRASVKLVKTCQEPAVGECQQCYCRPMWCLTCMGKWFASRQDPQRPDTWLASRVPCPTCR
Retrocopy ELEPCIGCMQTRASVKLVKTCQEPAVGECQQCYCRPMWCLTCMGKWFASRQDPQRPDTWLASRVPCPTCR

Parental  ARFCILDVCCVR
          ARFCILDVCCVR
Retrocopy ARFCILDVCCVR

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	13.80 RPM
SRP017611_kidney	0.00 RPM	16.75 RPM
SRP017611_liver	0.00 RPM	10.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1015 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1015 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000017329	1 retrocopy	retro_rnor_1015 ,