RetrogeneDB ID: retro_rnor_1382

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:3357438..3358197(-)
• Located in intron of: ENSRNOG00000012795

Retrocopy information

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

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_1382
GTGGAGGTGGTGGCGGCAGGATCAGTGTCAGGATTTGTCACTTGTGTCCTGATCAGCCTTTCGAACGTCATCGAGATCTG
TTTCCAGCTCCAGATTGAACACCTGTGTCCAAGTGACCCCAATGCCAAATACCACAGAATCTTCCAGGCGGCCAAGCATA
TTTTGTAAGAGGAGGGTCCAAGAGCGTCCTGGAAAGGACATGTTCCAGCCCAGATTCTGTCCATAGGCTACGGAGAGGTC
CAATTTTTGGCCTTTGAAGAACTGACTGAACTGCTTTACCGAGCCAACTTGTAATCAAACCCACCAATTCTCAGTGCACT
TTGTACATGGTGGCCTGTCTGCCGGTACAGCCACCCTCACCGTGCACCCTGTGGATGTGCTACACACCTGCCTAGCAGCT
CGGATCTATAACAATCTGCAAGAGGCCATACGGACCATGTATAGGACCAAGGGCCCCTTCATCTTCTACAAAGGCTTGAC
CCCCACCATGATCACCATCTTCCCCTCTATGGGCCTGCAGTTCTCCTGCTGCCACTCATTATTGAACCATGCCTATGACT
GGGTCATACCTACAGACAGAAGCAAACAGGGAACCTTAAAAACCTGCTTTGTAGCTGTGGATCTGGAGTCATCAGCAAGA
TCCTTACATATCCCCTGGACCTCTTCAAGAAGCCCCTACAGGTGGGTGGGTTTGAACATATCCTATCTGCCTTTCGCTGG
CTGCAGAGCTATGGGGACCTCCTAGACATCTCCACACAG

Alignment

ORF - retro_rnor_1382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.29 %
• Parental protein coverage: 80.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEVAVAGSVSGFVTRALISPLDVIKIRFQLQLERVCPSDPNAKYHGILQAAKQILQEEGPRAFWKGHVPA
          .EV..AGSVSGFVT..LIS...VI.I.FQLQ.E..CPSDPNAKYH.I.QAAK.IL.EEGPRA.WKGHVPA
Retrocopy VEVVAAGSVSGFVTCVLISLSNVIEICFQLQIEHLCPSDPNAKYHRIFQAAKHIL*EEGPRASWKGHVPA

Parental  QILSIGYGAVQFLAFEELTELLYQANL-YQTHQFSAHFVCGGLSAGTATLTVHPVDVLRTRLAAQGEPKI
          QILSIGYG.VQFLAFEELTELLY.ANL..QTHQFS.HFV.GGLSAGTATLTVHPVDVL.T.LAA.....I
Retrocopy QILSIGYGEVQFLAFEELTELLYRANL>NQTHQFSVHFVHGGLSAGTATLTVHPVDVLHTCLAA----RI

Parental  YSNLREAIRTMYRTEGPFVFYKGLTPTVIAIFPYAGLQFSCYRS-LKRAYDWIMPPD-GKQTGNLKNLLC
          Y.NL.EAIRTMYRT.GPF.FYKGLTPT.I.IFP..GLQFSC..S.L..AYDW..P.D..KQTGNLKNLLC
Retrocopy YNNLQEAIRTMYRTKGPFIFYKGLTPTMITIFPSMGLQFSCCHSLLNHAYDWVIPTD<QKQTGNLKNLLC

Parental  GCGSGVISKTLTYPLDLFKKRLQVRGFEHARSAFGQVRSYRGLLDLAQQ
          .CGSGVISK.LTYPLDLFKK.LQV.GFEH..SAF....SY..LLD...Q
Retrocopy SCGSGVISKILTYPLDLFKKPLQVGGFEHILSAFRWLQSYGDLLDISTQ

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	10.64 RPM
SRP017611_kidney	0.00 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_1382 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1382 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 ,