RetrogeneDB ID: retro_ttru_328

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1875:252778..253611(-)
• Located in intron of: ENSTTRG00000016958

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSTTRG00000000462
• Aliases: None
• Description: COP9 signalosome subunit 2 [Source:HGNC Symbol;Acc:30747]

Sequence

>retro_ttru_328
TTATTGATCTATATTTGTAGTTCAGCCATAAGAAATTATTCTGAAAAAGCTGTTAATTCTGTTCTTGAATTATATATCCA
CTGGAATATTTCCAAAAGAGAATTCAGATTTTTTTAAATGTCAGATGAATTCACTCTAGGAATTTTATGAAACAACAATT
AAAGTTCTGAAACATGCTAAGAATGATAGATTCTGGCTTAGGACAAGCATGAAGGTTAGAAAATTATATGAAGAATTGAG
AGGAATATGGAAAGCTTCAAAATATTTTATGCCAGTTTTATCAGTCATATTAGACTGATGATAAAGATAACCTGAAAAAG
GATATAAAATTATGAGATATATGACTTGGACATTCAAATGCACATAGAATAGGAATATAACAAAAAACTGAAAAAACTCT
GTAACTGGTTAGTTCTCATCCATCTGCCATCCCTCAACCATTTGATCATGGGAGTCATCAGATAAGTAAGGGGGAAAATG
CCCTTGAGATTAGGTGATTTTGAAAATTCACATGCTGAATTTTTGAAGCCTTCAAGAATGATAATAAATCGAGGAGTTCC
ATGTGAACCACTTGCTTAAAATATTTGGTCTTAGGAAATATGCTGAAGAACTTGGGAATAAATCCATTTGACTTGCCAGA
GGCCAAGCTGTACAAAAATGATCCAAAAATTCTAACAATGATGAATTCAGTAAGTTCCTATCAGAATAATGACATCGTTA
AATTTGAAAAGATTCTGAAAACAAATCACAGTAACGTTATGGATGATTCCTTCCTAAGAGAACACAGCAAAGAGCTTTTG
TAAAATATCGACACCCAAGTGCTGATAAAATTA

Alignment

ORF - retro_ttru_328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.19 %
• Parental protein coverage: 61.07 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LLTYIRSAVTRNYSEKSINSILD-YISTS---KQNSDFL-CQMDLLQEFYETTLEALKDAKNDRLWFKTN
          LL.YI.S...RNYSEK..NS.L..YIST....K.NSDF..CQM..L.EFYETT...LK.AKNDR.W..T.
Retrocopy LLIYICSSAIRNYSEKAVNSVLE>YISTGIFPKENSDFFKCQMNSL*EFYETTIKVLKHAKNDRFWLRTS

Parental  TKLGKLYLER-EEYGKLQKILRQLHQSCQTDDGEDDLK-KGTQLL-EIYALEIQMYTAQKNNKKLKALYE
          .K..KLY.E..EEYGKLQ.IL.Q..QS..TDD..D.LK.KG.....EIY.L.IQM......NKKLK.L..
Retrocopy MKVRKLYEEL>EEYGKLQNILCQFYQSY*TDD-KDNLK<KGYKIM<EIYDLDIQMHIE*EYNKKLKKLCN

Parental  QSLHIK-SAIPHP-LIMGVIRECGGKMHLREGEFEKAHTDF-FEAFKNYDESGSPRRTTCLKYLVLANML
          ....I..SAIP.P.LIMGVIR...GKM.LR.G.FE..H..F.FEAFKN...S.S...TTCLKYLVL.NML
Retrocopy WLVLIH<SAIPQP>LIMGVIR*VRGKMPLRLGDFENSHAEF<FEAFKNDNKSRSSM*TTCLKYLVLGNML

Parental  MKSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDPFIW--HIEELLRNIRT
          ...GINPFD..EAK.YKNDP.IL.M.N.VS.YQNNDI..FEKILKTNHSN.MD......H..ELL.NI.T
Retrocopy KNLGINPFDLPEAKLYKNDPKILTMMNSVSSYQNNDIVKFEKILKTNHSNVMDDSFLREHSKELL*NIDT

Parental  QVLIKL
          QVLIKL
Retrocopy QVLIKL

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_328 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_328 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013425	1 retrocopy	retro_btau_452,
Choloepus hoffmanni	ENSCHOG00000013375	7 retrocopies	retro_chof_1083, retro_chof_1288, retro_chof_2209, retro_chof_2371, retro_chof_2520, retro_chof_2550, retro_chof_678,
Callithrix jacchus	ENSCJAG00000001585	2 retrocopies	retro_cjac_3105, retro_cjac_3117,
Echinops telfairi	ENSETEG00000019523	2 retrocopies	retro_etel_2160, retro_etel_88,
Macaca mulatta	ENSMMUG00000009838	1 retrocopy	retro_mmul_62,
Monodelphis domestica	ENSMODG00000002466	1 retrocopy	retro_mdom_891,
Oryctolagus cuniculus	ENSOCUG00000006455	1 retrocopy	retro_ocun_1296,
Otolemur garnettii	ENSOGAG00000013284	1 retrocopy	retro_ogar_1513,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497,
Tursiops truncatus	ENSTTRG00000000462	1 retrocopy	retro_ttru_328 ,