RetrogeneDB ID: retro_rnor_12

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:202490046..202490988(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000016331
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Slc25a19
• Ensembl ID: ENSRNOG00000003918
• Aliases: None
• Description: mitochondrial thiamine pyrophosphate carrier [Source:RefSeq peptide;Acc:NP_001007675]

Sequence

>retro_rnor_12
ATGGTTGGCTATGACTCCAAAGCAGATGCCAGGAGTAACTCCAAGTTGGAGGTGGCGGTGGCGGGATCAGTGTCAGGATT
TGTCACTCGTGCCCTGATCAGCCCTTTGGATGTCATCAAGATCCGATTCCAGCTCCAGCTTGAACGTGTGTGTCCAAGTG
ACCCCGATGCCAAATACCACGGAATCTTCCAGGCGGCCAAGCAGATTATACAAGAAGAGGGTCCAAGAGCGTTCTGGAAA
GGACATGTTCCAGCCCAGATCCTGTCCATAGGCTATGGAGCCGTCCAATTTTTGGCCTTTGAAGAACTGACTGTACTGCT
TTACCAAGCCAACTTGTATCAAACCCACCAGTTCTCAGCACACTTTGTATGTGGAGGCCTGTCTGCCGGTACAGCCACCC
TCACCGTGCACCCCGTGGATGTCCTGCGCACCCGCCTTGCAGCTCAGGGGGAGCCCAATCTGCGAGAGGCTATAATCACC
ATGTATAGGACGGAGGGCCCCTTTGTCTTCTACAAAGGCTTGACTCCCACTGTGATCGCCATCTTCCCGTACGCGGGCTT
GCAGTTCTGCTACCGTTCCTTGAAACGCACCTATGACTGGGTCATGCCACCAGACAGAAAGCAAACAGGGAACCTTAAAA
ACCTGCTTTGTGGCTGTGGATCTGGAGTGATCAGCAAGACCCTTACGTATCCCCTGGACCTCTTCAAGAATCACCTGCAG
GTGCGGGGGTTTGAATATGCCCGATCTGCTTTTGGCCAAGTTCGGAGCTACAGGGGCCTCTTGGACCTCGCCCGGCAAGT
GTTACAACATGAAGACACCCGGGGCTTCTTCAAGGGCCTATCCCCCAGTCTGATGAAGGCTGCACTCTCCACTGGTTTCA
TGTTCTTCTGGTATGAGCTCTTCTGTAACCTCTTCCATTGCATAAGGAGGGAAGACAGATAG

Alignment

ORF - retro_rnor_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVGYDAKADARSNSKLEVAVAGSVSGFVTRALISPLDVIKIRFQLQLERVCPSDPNAKYHGILQAAKQIL
          MVGYD.KADARSNSKLEVAVAGSVSGFVTRALISPLDVIKIRFQLQLERVCPSDP.AKYHGI.QAAKQI.
Retrocopy MVGYDSKADARSNSKLEVAVAGSVSGFVTRALISPLDVIKIRFQLQLERVCPSDPDAKYHGIFQAAKQII

Parental  QEEGPRAFWKGHVPAQILSIGYGAVQFLAFEELTELLYQANLYQTHQFSAHFVCGGLSAGTATLTVHPVD
          QEEGPRAFWKGHVPAQILSIGYGAVQFLAFEELT.LLYQANLYQTHQFSAHFVCGGLSAGTATLTVHPVD
Retrocopy QEEGPRAFWKGHVPAQILSIGYGAVQFLAFEELTVLLYQANLYQTHQFSAHFVCGGLSAGTATLTVHPVD

Parental  VLRTRLAAQGEPKIYSNLREAIRTMYRTEGPFVFYKGLTPTVIAIFPYAGLQFSCYRSLKRAYDWIMPPD
          VLRTRLAAQGEP....NLREAI.TMYRTEGPFVFYKGLTPTVIAIFPYAGLQF.CYRSLKR.YDW.MPPD
Retrocopy VLRTRLAAQGEP----NLREAIITMYRTEGPFVFYKGLTPTVIAIFPYAGLQF-CYRSLKRTYDWVMPPD

Parental  GKQTGNLKNLLCGCGSGVISKTLTYPLDLFKKRLQVRGFEHARSAFGQVRSYRGLLDLAQQVLQHEGTRG
          .KQTGNLKNLLCGCGSGVISKTLTYPLDLFK..LQVRGFE.ARSAFGQVRSYRGLLDLA.QVLQHE.TRG
Retrocopy RKQTGNLKNLLCGCGSGVISKTLTYPLDLFKNHLQVRGFEYARSAFGQVRSYRGLLDLARQVLQHEDTRG

Parental  FFKGLSPSLMKAALSTGFMFFWYELFCNLFHCIRREDR
          FFKGLSPSLMKAALSTGFMFFWYELFCNLFHCIRREDR
Retrocopy FFKGLSPSLMKAALSTGFMFFWYELFCNLFHCIRREDR

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	0.07 RPM	10.64 RPM
SRP017611_kidney	0.07 RPM	11.93 RPM
SRP017611_liver	0.00 RPM	3.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_12 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_12 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000008772	1 retrocopy	retro_meug_338,
Rattus norvegicus	ENSRNOG00000003918	2 retrocopies	retro_rnor_12 , retro_rnor_1382,