RetrogeneDB ID: retro_rnor_1917

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:124564308..124566233(-)
• Located in intron of: ENSRNOG00000008629

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmf1
• Ensembl ID: ENSRNOG00000005851
• Aliases: None
• Description: TATA element modulatory factor 1 [Source:RefSeq peptide;Acc:NP_446123]

Sequence

>retro_rnor_1917
GTGAGCCAGACAGTTGAATTTCTGAATGAGAAGCTAGAAAAGAGGGAGACTCAATTATTGTCACTTAGTAAGGAAAAGGC
ACTTCTAGCTTATGATAACCTGAAGGATGAAATGTTCAGAGTAAAAGAAGAAAGTGGTAGCATTTCTTCCCTGAAAGATG
AGTTTACCCAGAGGATCGCAGAAGCAGAAAGGAAAGCTCAACTCGCCTGAAAAGAGAGAGACACTGCGAAGAAGGAAATG
AAAACCATGAAGGAAGAACTTGCCTCTAGATTAAATAGTAGTCAGACTGCAGACCTTCTGAAGGAAAAGGATGAACAGAT
TCAAGGCTTAATGGAAGAAGGAGAAAAACTTTCGAAGCAGCAGCTGCATAATTCCAACATGATTAAGAAATTAAGAGCTA
AGGATAAAGACAATGAAAGTGTTATTGCAAAGCTGAAGAAAAAAGCTAAGGAGCTGGAAGAGGAGCTACAGCATTTAAGA
CAGGTCCTTGATGGCAAAGAAGAGGTTGAAAAACAACATAGAGAAAACATTAAAAAACTAAATTCTGTAGTAGAACGCCA
GGAAAAAGATCTTGGCCGACTTCAGGTAGACATGAATGAACTTGAAGAAAAGAGCCGAAGTCCTCAGGCTGCCCTAGACA
GTGCCTACAGAGAACTTACTGATCTTCACAAAGCCAATGCTGCTAAGGACACTGAGGTACAGGCTGCTCTGAGGCGTGAG
ATGAAAGTAAAGAAGAACTTTCTGGGGCACTGGAGAAGGCCCAGGAAGAAGCCCGTCAGCAGCAAGAGACTTTAGCACTT
CAGGTGGGGGACCTTAGGCTAGCGCTGCAACGGGCAGAGCAAGCAGCTGCCAGGAAAGAGGATTACTTACGCCATGAGAT
CAGTGAACTTCAGCAGAGACTCCAAGAAGCAGAGAATCGAAACCAGGAGCTGAGTCAAAGTGTTTCATCAACAACAAGAC
CTTTGCTTCGACAGATAGAAAATTTACAAGCAACTCTAGGATCCCAGACATCGTCATGGGAGATGCTAGAGAAGAATCTT
TCTGATCGGCTCGGTGAATCACAGACCTTGTTGGCTGCAGCAGTTGAAAGAGAACGTGCAGCTACGGAAGAACTCCTAGC
CAACAAAATCCAGATGTCTTCAGTGGAGTCGCAGAATGCATTACTACGACAGGAAAACAGTAGACTGCAGGCCCAGCTAG
AGTCAGAGAAAAATAAATTAAGAAAACTAGAGGATGAAAATAGCCGGTACCAGGTTGAATTAGAAAATCTAAAAGATGAA
TATGTAAGAACACTTGAAGAGGCAAGGAAAGAAAAGACACTTTTGAGCAGTCAGTTAGAAATGGAAAGAATGAAAGTTGA
ACAAGAAAGGAAGAAAACCATTTTCACTCAAGAAACACTAAAAGAAAAGGACCACAAGCCGTTTTCCGTTTCTAGTACTC
CCACCATGTCACGATCCAGTTCTCTAAGTGGAGTAGATATGGCAGGGCTGCAGACATCCTTCCTATCTCAGGATGAGTCT
CACGACCATTCATTTGGGCCAGTGTCTACGTCAGCCAGTGGAAGCAATCTTTATGAAGCTGTAAGGATGGGAGCCGGATC
AAGCATTATCGAAAATCTTCAGTCTCAGCTAAAGCTGAGGGAAGGAGAAATTAGTCATTTACAGCTAGAAATTAGTAACC
TAGAAAAAACTCGATCCATAATGTCTGAAGAGCTAGTTAAATTGACAAATCAGAATGATGAACTTGAGGAGAAAGTGAAA
GAGATACCCAAGCTTCGAGTTCAGCTGCGAGATTTGGATCAAAGATACAACACTATTCTGCAGATGTATGGAGAAAAAGC
AGAAGCAGAGGAACTTCGCCTGGATCTTGATGTAAAAAATATGTATAAAACTCAAATAGATGAACTTCTAAGACAAAGAC
TCAGC

Alignment

ORF - retro_rnor_1917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.99 %
• Parental protein coverage: 59.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGKTVEFLNEKLEKRETQLLSLSKEKALLEEAYDNLKDEMFRVKEESSSISSLKDEFTQRIAEAERKAQL
          V..TVEFLNEKLEKRETQLLSLSKEKALL..AYDNLKDEMFRVKEES.SISSLKDEFTQRIAEAERKAQL
Retrocopy VSQTVEFLNEKLEKRETQLLSLSKEKALL--AYDNLKDEMFRVKEESGSISSLKDEFTQRIAEAERKAQL

Parental  ACKERDTAKKEMKTMKEELASRLNSSQTADLLKEKDEQIQGLMEEGEKLSKQQLHNSNMIKKLRAKDKDN
          A.KERDTAKKEMKTMKEELASRLNSSQTADLLKEKDEQIQGLMEEGEKLSKQQLHNSNMIKKLRAKDKDN
Retrocopy A*KERDTAKKEMKTMKEELASRLNSSQTADLLKEKDEQIQGLMEEGEKLSKQQLHNSNMIKKLRAKDKDN

Parental  ESVIAKLKKKAKELEEELQHLRQVLDGKEEVEKQHRENIKKLNSVVERQEKDLGRLQVDMNELEEKSRST
          ESVIAKLKKKAKELEEELQHLRQVLDGKEEVEKQHRENIKKLNSVVERQEKDLGRLQVDMNELEEKSRS.
Retrocopy ESVIAKLKKKAKELEEELQHLRQVLDGKEEVEKQHRENIKKLNSVVERQEKDLGRLQVDMNELEEKSRSP

Parental  QAALDSAYRELTDLHKANAAKDSEVQEAALRREMK-AKEELSGALEKAQEEARQQQETLALQVGDLRLAL
          QAALDSAYRELTDLHKANAAKD.EVQ.AALRREMK..KEELSGALEKAQEEARQQQETLALQVGDLRLAL
Retrocopy QAALDSAYRELTDLHKANAAKDTEVQ-AALRREMK<SKEELSGALEKAQEEARQQQETLALQVGDLRLAL

Parental  QRAEQAAARKEDYLRHEISELQQRLQEAENRNQELSQSVSSTTRPLLRQIENLQATLGSQTSSWEMLEKN
          QRAEQAAARKEDYLRHEISELQQRLQEAENRNQELSQSVSSTTRPLLRQIENLQATLGSQTSSWEMLEKN
Retrocopy QRAEQAAARKEDYLRHEISELQQRLQEAENRNQELSQSVSSTTRPLLRQIENLQATLGSQTSSWEMLEKN

Parental  LSDRLGESQTLLAAAVERERAATEELLANKIQMSSVESQNALLRQENSRLQAQLESEKNKLRKLEDENSR
          LSDRLGESQTLLAAAVERERAATEELLANKIQMSSVESQNALLRQENSRLQAQLESEKNKLRKLEDENSR
Retrocopy LSDRLGESQTLLAAAVERERAATEELLANKIQMSSVESQNALLRQENSRLQAQLESEKNKLRKLEDENSR

Parental  YQVELENLKDEYVRTLEEARKEKTLLSSQLEMERMKVEQERKKTIFTQETLKEKEHKPFSVSSTPTMSRS
          YQVELENLKDEYVRTLEEARKEKTLLSSQLEMERMKVEQERKKTIFTQETLKEK.HKPFSVSSTPTMSRS
Retrocopy YQVELENLKDEYVRTLEEARKEKTLLSSQLEMERMKVEQERKKTIFTQETLKEKDHKPFSVSSTPTMSRS

Parental  SSLSGVDMAGLQTSFLSQDESHDHSFGPMSTSASGSNLYEAVRMGAGSSIIENLQSQLKLREGEISHLQL
          SSLSGVDMAGLQTSFLSQDESHDHSFGP.STSASGSNLYEAVRMGAGSSIIENLQSQLKLREGEISHLQL
Retrocopy SSLSGVDMAGLQTSFLSQDESHDHSFGPVSTSASGSNLYEAVRMGAGSSIIENLQSQLKLREGEISHLQL

Parental  EISNLEKTRSIMSEELVKLTNQNDELEEKVKEIPKLRVQLRDLDQRYNTILQMYGEKAEAEELRLDLDVK
          EISNLEKTRSIMSEELVKLTNQNDELEEKVKEIPKLRVQLRDLDQRYNTILQMYGEKAEAEELRLDLDVK
Retrocopy EISNLEKTRSIMSEELVKLTNQNDELEEKVKEIPKLRVQLRDLDQRYNTILQMYGEKAEAEELRLDLDVK

Parental  NMYKTQIDELLRQRLS
          NMYKTQIDELLRQRLS
Retrocopy NMYKTQIDELLRQRLS

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	1.08 RPM	41.12 RPM
SRP017611_kidney	0.84 RPM	70.62 RPM
SRP017611_liver	0.20 RPM	29.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1917 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1917 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1917 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	ENSRNOG00000005851	1 retrocopy	retro_rnor_1917 ,