RetrogeneDB ID: retro_ttru_289

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1778:445186..446142(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XRCC6
• Ensembl ID: ENSTTRG00000006749
• Aliases: None
• Description: X-ray repair complementing defective repair in Chinese hamster cells 6 [Source:HGNC Symbol;Acc:4055]

Sequence

>retro_ttru_289
ATGTCAGGGTGGGAGTCTTATTACAAAAATCAGGGTGATGAGGAAGAAGAAGATCAAGAGGAGGGCCTTGAAGCAGGTGG
AGATTATAAATATTCAGGAAGACATAGTTTGATTTTTTTGATTGATGCTTCCGAGACCATGTTTGAAACTCAGGATGAAG
ATGAGTCGACTCCTTTTGACATTAGCATCCAGTATATCTGGAGTGTATACACCAATAAGATCATAAGCAGTGATCGAGAT
CTCTTGGCAGTGGTGTTCTATGGTACCAATAAGGACAAAAATTCAGTGAATTTCAAAAATATTTACGTCTTGCAGGAATT
GGGTAATCCAGGTGCTAAATGAGTGCTAGAGCTTGACCACTTTAAGGGGCAGGAGGGGAAGAAACATTTCCAAGACCTAG
TTGGCCATGGATCTGACTACTCCCTAAGTGAAGTACTGTGGGTCTATGCCAACCTCTTTAGCGATGTCCAGTTCAAGATG
AGCCATAAGAGGATCATGCTTTTCACCAATAAAGATGACCCCCACAGCAATGACAGTGCCAAAGCCAGCCGGGCCAGGAT
CAAAGCTGGAGATCTCCGTGACACAGGTATATTCCTTGCCTTGTTGCACCTAAAGAAACGTGGGGGCTTTAACATATCCT
TGTTCTACAGAGATATTATCAGCATAGCAGAGGATGAGGACATAGGGGTCCACTTTGAGGAGTTGAGCAAGCTCAAAGAC
CTGTTGAGGAAGGTTTGTGCCAAGGAGACCAGGAAGCGCGTGCTCTACAGGTTGAAGCTTAAGCCCAACGAAGATGTAGC
GCTTACTGTTGGCAATTATAATATGGTCCAGAGGCTCTCAAACCTTCTCCAGTGAGGCTTTATCGGGAAACAAATGAACC
AGTGAAAACCAAGACCCGGACACTTAATGTAAATACAGGCAGTTTGCTTTTGCCTAGCAACACCAAGAGGTCCCAG

Alignment

ORF - retro_ttru_289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 52.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGWESYYKNQGDEEEEDQEEGLEEGGDYKYSGRDSLIFLIDASEAMFETQDEDELTPFDMSIQCIRSVY
          MSGWESYYKNQGDEEEEDQEEGLE.GGDYKYSGR.SLIFLIDASE.MFETQDEDE.TPFD.SIQ.I.SVY
Retrocopy MSGWESYYKNQGDEEEEDQEEGLEAGGDYKYSGRHSLIFLIDASETMFETQDEDESTPFDISIQYIWSVY

Parental  TSKIISSDRDLLAVVFYGTKKDKNSVNFKNIYVLQELDNPGAKRVLELDRFKGQEGKKHFQDLIGHGSDY
          T.KIISSDRDLLAVVFYGT.KDKNSVNFKNIYVLQEL.NPGAK.VLELD.FKGQEGKKHFQDL.GHGSDY
Retrocopy TNKIISSDRDLLAVVFYGTNKDKNSVNFKNIYVLQELGNPGAK*VLELDHFKGQEGKKHFQDLVGHGSDY

Parental  SLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDDPHGNDSAKASRARTKAGDLRDTGIFLDLLHLRKRGGF
          SLSEVLWV.ANLFSDVQFKMSHKRIMLFTN.DDPH.NDSAKASRAR.KAGDLRDTGIFL.LLHL.KRGGF
Retrocopy SLSEVLWVYANLFSDVQFKMSHKRIMLFTNKDDPHSNDSAKASRARIKAGDLRDTGIFLALLHLKKRGGF

Parental  DISLFYRDIISIAEDEDIGVHFEESSKLEDLSRKVRAKETRKRVLCRLKLKLNKDVALTVGIYNMVQK-A
          .ISLFYRDIISIAEDEDIGVHFEE.SKL.DL.RKV.AKETRKRVL.RLKLK.N.DVALTVG.YNMVQ..A
Retrocopy NISLFYRDIISIAEDEDIGVHFEELSKLKDLLRKVCAKETRKRVLYRLKLKPNEDVALTVGNYNMVQR<A

Parental  LKPSPVRLYRETNEPVKTKTRTFNVNTGSLLLPSDTKRSQ
          LKPSPVRLYRETNEPVKTKTRT.NVNTGSLLLPS.TKRSQ
Retrocopy LKPSPVRLYRETNEPVKTKTRTLNVNTGSLLLPSNTKRSQ

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_289 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_289 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 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000196419	4 retrocopies	retro_hsap_4066, retro_hsap_4880, retro_hsap_4913, retro_hsap_511,
Gorilla gorilla	ENSGGOG00000015885	2 retrocopies	retro_ggor_3067, retro_ggor_471,
Macaca mulatta	ENSMMUG00000001856	2 retrocopies	retro_mmul_2346, retro_mmul_430,
Nomascus leucogenys	ENSNLEG00000015610	3 retrocopies	retro_nleu_1552, retro_nleu_2287, retro_nleu_2676,
Pongo abelii	ENSPPYG00000011876	1 retrocopy	retro_pabe_3821,
Tupaia belangeri	ENSTBEG00000011736	3 retrocopies	retro_tbel_1474, retro_tbel_1523, retro_tbel_3859,
Tursiops truncatus	ENSTTRG00000006749	1 retrocopy	retro_ttru_289 ,