RetrogeneDB ID: retro_ttru_958

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_79:175355..176129(-)
• Located in intron of: ENSTTRG00000005374

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRYZ
• Ensembl ID: ENSTTRG00000010471
• Aliases: None
• Description: crystallin, zeta (quinone reductase) [Source:HGNC Symbol;Acc:2419]

Sequence

>retro_ttru_958
ATGGTGACTGAACAGAGGTTGATGCGAGCTATTAGAGTTTTTTAATTTGTGGACCAGAAGTGATGAAACTCCAGTCGGAT
GTTGCCATACCGATTCCAAAAGACCATCAGGTTCTAATCAAAGTCCAAGCATGTAGTGTAAACCCAGTGGACACACAAAT
TCACTCTGGTACCTACAGTGGAAAACCACTTCCACCTTATACTCCTGGATTAGATGTGGCTGGGATAACAGAAGCTGTTG
GAGAAAGTGTATCTGCTTTCAAGAAAAGTGACAGAGTTTTCACTACCAGCATGATCTCTGAGGGCTACGCAGAGTATGCT
CTGGCAGCCAATTACCCTGTTTACACACTGCCGGAAAAACTGGACTTTAAACAAGGAGCTGCCATCAGTATCCCGTATTT
TACTGCTTATTGAGCTCTGCTCCACAGTGCCTGTGTGAAAGCTGGAGAAAGTGTTCTGGTTCATGAAGCTAGTGGAGGAG
TTGGGATAGCAGCATGCCAGACTGCTAGAGTTGATGGCTTAAAAGTTTTGGGCACAGCTGGTACTGAGGAAGGACAAAAC
ACTGTTTTGCAAAATGGGGCCCACGAAGTGTTTAATCACAGAGAAACTAATTATATTGATATAATTAAGAAATCTTTTGG
TGAAAAGGAGTTGATGTGATTATTGAAATGTTAACTAATGTAAATCTTAGCAATGATTTGAATCTTTGTCACATGGAGGA
CGAGTAATAGTTGTTGGCAGCAGAGGTCCTGTTGAAATAAACCCACGGGAGACA

Alignment

ORF - retro_ttru_958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.5 %
• Parental protein coverage: 78.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATGQKLMRAIRVFEFG-GPEVLKLQSNVAIPIPKDHQVLIKVQACGVNPVDTYIRSGTYSRKPLLPYTP
          M.T.Q.LMRAIRVF.F..GPEV.KLQS.VAIPIPKDHQVLIKVQAC.VNPVDT.I.SGTYS.KPL.PYTP
Retrocopy MVTEQRLMRAIRVF*FV<GPEVMKLQSDVAIPIPKDHQVLIKVQACSVNPVDTQIHSGTYSGKPLPPYTP

Parental  GLDVAGIIEAVGESVSAFKKGDRVFTTSTISGGYAEYALAADHTVYTLPEKLDFKQGAAIGIPYFTAYRA
          GLDVAGI.EAVGESVSAFKK.DRVFTTS.IS.GYAEYALAA...VYTLPEKLDFKQGAAI.IPYFTAY.A
Retrocopy GLDVAGITEAVGESVSAFKKSDRVFTTSMISEGYAEYALAANYPVYTLPEKLDFKQGAAISIPYFTAY*A

Parental  LLHSAHVKAGESVLVHGASGGVGIAACQIARAYGLKVLGTAGTEEGQKIVLQNGAHEVFNHKEANYIDKI
          LLHSA.VKAGESVLVH.ASGGVGIAACQ.AR..GLKVLGTAGTEEGQ..VLQNGAHEVFNH.E.NYID.I
Retrocopy LLHSACVKAGESVLVHEASGGVGIAACQTARVDGLKVLGTAGTEEGQNTVLQNGAHEVFNHRETNYIDII

Parental  KKSVGE-KGVDVIIEMLANVNLSNDLNL-LSHGGRVIVVGSRGPIEINPRDT
          KKS.GE.KGVDVIIEML.NVNLSNDLNL.LSHGGRVIVVGSRGP.EINPR.T
Retrocopy KKSFGE<KGVDVIIEMLTNVNLSNDLNL<LSHGGRVIVVGSRGPVEINPRET

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_958 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_958 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 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003162	1 retrocopy	retro_btau_1433,
Canis familiaris	ENSCAFG00000020404	1 retrocopy	retro_cfam_870,
Choloepus hoffmanni	ENSCHOG00000005167	1 retrocopy	retro_chof_1772,
Felis catus	ENSFCAG00000030626	1 retrocopy	retro_fcat_1907,
Homo sapiens	ENSG00000116791	1 retrocopy	retro_hsap_3884,
Loxodonta africana	ENSLAFG00000011371	1 retrocopy	retro_lafr_527,
Macaca mulatta	ENSMMUG00000014593	2 retrocopies	retro_mmul_1026, retro_mmul_1728,
Mustela putorius furo	ENSMPUG00000010969	1 retrocopy	retro_mputfur_119,
Mus musculus	ENSMUSG00000028199	1 retrocopy	retro_mmus_1314,
Nomascus leucogenys	ENSNLEG00000009543	2 retrocopies	retro_nleu_1890, retro_nleu_3115,
Otolemur garnettii	ENSOGAG00000011586	1 retrocopy	retro_ogar_179,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165,
Pan troglodytes	ENSPTRG00000000865	1 retrocopy	retro_ptro_1598,
Tupaia belangeri	ENSTBEG00000016750	3 retrocopies	retro_tbel_1665, retro_tbel_2353, retro_tbel_3800,
Tarsius syrichta	ENSTSYG00000004193	2 retrocopies	retro_tsyr_1218, retro_tsyr_1884,
Tursiops truncatus	ENSTTRG00000010471	2 retrocopies	retro_ttru_555, retro_ttru_958 ,