RetrogeneDB ID: retro_rnor_244

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:82456665..82457364(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000019427
• Aliases: Tescl, RGD1311676
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tesc
• Ensembl ID: ENSRNOG00000001128
• Aliases: Tesc, RGD1566317
• Description: Protein Tesc [Source:UniProtKB/TrEMBL;Acc:D3ZTN1]

Sequence

>retro_rnor_244
ATGGGTGTCTCACATTCGTCCAGGGAGGAGTGGGAGCGCGAAAGCAGGACCGACTTATGGTGGGCGCACATCCAGGAGGC
GTTCATGAAGAAGTGCGACTTCAGCTGGGACCAGATCAAGCAGTTGCACCAGAGGTTCCGGCTGCTGAGCGGGGACCAGC
CCACCCTCCGACCCGAGAACTTCGACAACGTCCTGGACCTGGAGTTCAACCCGATCCGCTCCAGGATCGTCCGTGCCTTC
TTCGACAACCGGAACCTGGGCAAAGGGACCAGCGGGCTGGCGGAGGAGATCACCTTCCAGGACTTCCTAACCATCATCTC
CTACTTCCGGCCGCTGGAGCCCCGGCCCAACAAGGAGGAGGCAGAGCAGTACCGCAAAGAGAAGATGCAGTTCCTCTTCA
ACATGTACGACCAGGACGGCGATGGGATCATCACCCTGCAGGAGTACCGCCGGGTGGTGGAGGACCTGCTGTCGGCGAAC
CCGCAGGCGGAGACAGCCACTGTGCGCTCCGTCGCCAACTCCATCGCGCGGGTCGCCTTGATGGAGGCGTCCAGGGCATC
CGACCAGCCTCTGAATGAGGACGAGCCATACGAGGGCATCACCTTCGAGGACTTCTTCAAGACCTGGCAGAGCCTCGAAT
TGGAAGTCAAGATGCAAGTCAGCTTCCTGAACCTACAAGCCATGGCCTTCTGCCAGTGA

Alignment

ORF - retro_rnor_244 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.7 %
• Parental protein coverage: 92.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTGFSSDQIEQLHRRFKQLSGDQPTIRKENFNNVPDLELNPIRSKIVRAFFDNRNLRKGSSGLADEINFE
          K..FS.DQI.QLH.RF..LSGDQPT.R.ENF.NV.DLE.NPIRS.IVRAFFDNRNL.KG.SGLA.EI.F.
Retrocopy KCDFSWDQIKQLHQRFRLLSGDQPTLRPENFDNVLDLEFNPIRSRIVRAFFDNRNLGKGTSGLAEEITFQ

Parental  DFLTIMSYFRPIDTTLGEEQVELSRKEKLKFLFHMYDSDSDGRITLEEYRNVVEELLSGNPHIEKESARS
          DFLTI.SYFRP.......E..E..RKEK..FLF.MYD.D.DG.ITL.EYR.VVE.LLS.NP..E....RS
Retrocopy DFLTIISYFRPLEPRPNKEEAEQYRKEKMQFLFNMYDQDGDGIITLQEYRRVVEDLLSANPQAETATVRS

Parental  IADG----AMMEAASVCVGQMEPDQVYEGITFEDFLKIWQGIDIETKMHIRFLNMETIALC
          .A......A.MEA..........D..YEGITFEDF.K.WQ....E.KM...FLN....A.C
Retrocopy VANSIARVALMEASRASDQPLNEDEPYEGITFEDFFKTWQSLELEVKMQVSFLNLQAMAFC

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	26.03 RPM
SRP017611_kidney	0.00 RPM	8.79 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_244 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_244 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_244 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_212

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012517	1 retrocopy	retro_amel_1156,
Canis familiaris	ENSCAFG00000009300	1 retrocopy	retro_cfam_1310,
Callithrix jacchus	ENSCJAG00000009509	1 retrocopy	retro_cjac_3226,
Equus caballus	ENSECAG00000011177	1 retrocopy	retro_ecab_1005,
Felis catus	ENSFCAG00000002633	1 retrocopy	retro_fcat_1841,
Myotis lucifugus	ENSMLUG00000001775	1 retrocopy	retro_mluc_531,
Mus musculus	ENSMUSG00000029359	1 retrocopy	retro_mmus_212,
Rattus norvegicus	ENSRNOG00000001128	1 retrocopy	retro_rnor_244 ,