RetrogeneDB ID: retro_rnor_734

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:24789867..24790369(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tpm1
• Ensembl ID: ENSRNOG00000018184
• Aliases: Tpm1, Alpha-tm, Tma2, Tmsa
• Description: Tropomyosin alpha-1 chain [Source:UniProtKB/Swiss-Prot;Acc:P04692]

Sequence

>retro_rnor_734
AAGAAAGCCACGTATGCTGAGGCTGATGTAGCTTCTCTGAAAAGACACATCCTGCTGTTTGAAGAGGAGTGGGATTGTAT
CCCGGAACGTTTGACCACAGCTCTGCAGAAGCTGGGGAAGCTGAGAAGGCCGCGGAAGAGTGTGAGAGAGGCATGAATGT
CAGTGAAAGCCGAGCCCAAAAGGATGAAGAAAAGACAGAAATTCTGGAAATCCGTCTGAAGGAAGCCAAGCATATTGCTC
AAGACGCTGACTGCAAATATGAAGAGGTGGCCGGTAAACTGGTCATTATCAATGATAGTGGTCATTGTAGATAGTGATCA
GAGGAATGTTCGGAAGAGTGGGCTGTGCTCTCAGAGGGCCAAGGTCAGCAGCTGTCAGATCTTGAATGCATTAATGGCTG
CAAAGTATAGTACTCTCAGGAGGAGGCAAATAGGAGGAGTTCAAGGTTCTCTCTGACAAGGTAAAGGAGGCTGAGACTCG
GGCCAAGTTTTTAGAGATCAGT

Alignment

ORF - retro_rnor_734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.05 %
• Parental protein coverage: 59.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLE-EAEKAADESERGMKVIESRAQKDEEKMEIQ
          KKAT.AEADVASL.R.I.L.EEE.D...ERL.TALQKL..EAEKAA.E.ERGM.V.ESRAQKDEEK.EI.
Retrocopy KKATYAEADVASLKRHILLFEEEWDCIPERLTTALQKLG<EAEKAAEECERGMNVSESRAQKDEEKTEIL

Parental  EIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEAQAEKY
          EI.LKEAKHIA.DAD.KYEEVA.KLVII..D........E......A.L.E........L.........Y
Retrocopy EIRLKEAKHIAQDADCKYEEVAGKLVII-NDSGHCR**SEECSEEWAVLSEGQGQQLSDLECINGCKV*Y

Parental  SQKE-DKYEEEIKVLSDKLKEAETRAEFAERS
          SQ.E..K.EE..KVLSDK.KEAETRA.F.E.S
Retrocopy SQEE<GK*EE-FKVLSDKVKEAETRAKFLEIS

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	110.07 RPM
SRP017611_kidney	0.00 RPM	99.86 RPM
SRP017611_liver	0.00 RPM	43.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_734 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_734 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_734 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016966	1 retrocopy	retro_cfam_2167,
Choloepus hoffmanni	ENSCHOG00000012788	11 retrocopies	retro_chof_1194, retro_chof_1272, retro_chof_1360, retro_chof_1789, retro_chof_1829, retro_chof_2309, retro_chof_346, retro_chof_399, retro_chof_412, retro_chof_770, retro_chof_967,
Macropus eugenii	ENSMEUG00000014581	2 retrocopies	retro_meug_1944, retro_meug_2161,
Rattus norvegicus	ENSRNOG00000016731	1 retrocopy	retro_rnor_1520,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Rattus norvegicus	ENSRNOG00000018184	1 retrocopy	retro_rnor_734 ,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Tursiops truncatus	ENSTTRG00000003762	1 retrocopy	retro_ttru_446,
Vicugna pacos	ENSVPAG00000003277	1 retrocopy	retro_vpac_424,