RetrogeneDB ID: retro_ttru_446

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2324:20537..21185(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM1
• Ensembl ID: ENSTTRG00000003762
• Aliases: None
• Description: tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]

Sequence

>retro_ttru_446
GACGCGGGGGAGAGGTCTGAGCGCCCCCTGCGGAAGTGTAGGAGAAAGGCGGCCCGGGAACAGGCTGAGGCGGCCTCCTT
GAACCATAGGGTCCAGCTGGTTGAAGAGCTGGACTGCGCTCAAGAGCGCCTGGCCGCTGCCCTGAAAATGCTGGAGGAAG
CCGAGAAAGCTGCTGATGACAGCGAGAGAGACATGAAGGTTACTGAAAACCGAGGCTTAAAAGAGGAAATAAAAATGGAG
CTCCAGGAAATCCAATTCAAAGAAGCTAAGCACATTGCAGAAGAGTATGAAGAGGTGGCTCTTAGGTTGGTGATTATTGA
GGGAGACTTGGAAGTCACAGAGGAGCGAGCTGAGCTGGCAGAGTCCGGTTGCTGAGAGACGGATGAGCAGGTCAGACTGA
TGGACCAGAAGCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACATATGAGGAAGAGAGAAAGAT
TCTTACTGATAAACTCAAGGAGGCAGAGACCCGTGCTGAGTGTGCTGAGAGATCGGTAACCAAGCTGGAAAAGACGGTGA
TTTGGAAGATGAACTGATATGCACCAAAGAGGAGCACCTCTGTACACAAAGGATGCTGGACCAGACTCTGCTTGACCTGG
ATGAGATG

Alignment

ORF - retro_ttru_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.78 %
• Parental protein coverage: 68.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIE
          .A.......L.....KA....A..ASLN.R.QLVEE.LD.AQERLA.AL..LEEAEKAAD.SER.MKV.E
Retrocopy DAGERSERPLRKCRRKAAREQAEAASLNHRVQLVEE-LDCAQERLAAALKMLEEAEKAADDSERDMKVTE

Parental  SRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVT
          .R..K.E.KME.QEIQ.KEAKHIAE.....YEEVA..LVIIE.DLE..EERAEL.E..C.E..E......
Retrocopy NRGLKEEIKMELQEIQFKEAKHIAEE----YEEVALRLVIIEGDLEVTEERAELAESGC*ETDEQVRLMD

Parental  NNLKSLEAQAE-KYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSI-DDLEEKVAHAKEENLS
          ..LK.L.A.AE.K...K...YEEE.K.L.DKLKEAETRAE.AERSVTKLEK...D...E......E..L.
Retrocopy QKLKCLSA-AE>KSTLKKKTYEEERKILTDKLKEAETRAECAERSVTKLEKTV<DLEDELICTKEE-HLC

Parental  MHQMLDQTLLELNNM
          ...MLDQTLL.L..M
Retrocopy TQRMLDQTLLDLDEM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_446 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_446 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 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,
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200, retro_cjac_691,
Macropus eugenii	ENSMEUG00000014581	2 retrocopies	retro_meug_1944, retro_meug_2161,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624,
Rattus norvegicus	ENSRNOG00000018184	1 retrocopy	retro_rnor_734,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Tursiops truncatus	ENSTTRG00000003762	1 retrocopy	retro_ttru_446 ,
Tursiops truncatus	ENSTTRG00000014542	2 retrocopies	retro_ttru_504, retro_ttru_839,
Vicugna pacos	ENSVPAG00000003277	1 retrocopy	retro_vpac_424,