RetrogeneDB ID: retro_crei_1

Retrocopy location

• Organism: Chlamydomonas reinhardtii
• Coordinates: BK000554:160164..161640(-)
• Located in intron of: DAA01471

Retrocopy information

• Ensembl ID: DAA00958
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: CHLREDRAFT_78348
• Aliases: None
• Description: None

Sequence

>retro_crei_1
ATGCCTTGGGGCATATTAATTCCACTTACTATGAGTGATTCTATTGAAACAAAAAACATGGGACGTATTGTACAAATTAT
TGGTCCTGTTTTAGATATCGTATTTGCTAAAGGCCAAGTACCAAATATTTACAACGCTCTAACTATTCGTGCTAAAAACT
CAGCAGGTACAGAAATGGCTGTTACTTGTGAAGTTCAACAACTTTTAGGTGATAACTGTGTACGTGCAGTTTCTATGAAC
CCAACAGAAGGTTTAATGCGTGGTATGGAAGTTGTAGATACTGGTAAACCGTTAAGTGTTCCTGTAGGTAAAGTAACTTT
AGGACGTATTTTCAACGTTCTAGGTGAACCTGTAGATAACATGGGTAATGTTAAAGTTGAAGAAACTTTACCAATTCACC
GTACAGCTCCTGCTTTCGTTGATTTAGATACTCGTTTATCAATTTTTGAAACAGGTATTAAAGTTGTAGACCTTTTAGCT
CCATACCGTCGTGGTGGTAAAATTGGTCTTTTCGGTGGTGCTGGTGTAGGCAAAACAGTTTTAATTATGGAACTGATCAA
CAACATTGCTAAAGCACACGGTGGTGTTTCTGTATTTGCTGGTGTTGGTGAACGTACACGTGAAGGTAACGACCTTTACA
CAGAAATGAAAGAATCTGGTGTTATTGTTGAAAAGAACTTATCTGATTCAAAAGTAGCTCTTGTATACGGTCAAATGAAC
GAACCACCAGGTGCTCGTATGCGTGTTGCTTTAACAGCTTTAACAATGGCTGAATATTTCCGTGATGTTAACAAACAAGA
CGTATTATTCTTCATTGATAACATTTTCCGTTTCGTACAAGCTGGTGCTGAAGTATCTGCTTTATTAGGTCGTATGCCAT
CAGCTGTAGGTTACCAACCTACTTTAGCTACAGAAATGGGTGGTCTTCAAGAACGTATTACTTCAACTAAAGATGGTTCT
ATCACATCGATTCAGGCTGTATATGTACCTGCAGATGACCTTACTGACCCTGCTCCTGCTACAACATTCGCTCACTTAGA
TGCTACTACAGTACTTTCTCGTAACTTAGCTGCTAAAGGTATTTACCCTGCGGTTGACCCATTAGAATCAACTTCAACTA
TGTTACAACCGTGGATTCTTGGTGAAAAACACTATGATTCTGCACAAAGCGTAAAAAAAACTTTACAACGTTACAAAGAA
TTACAAGATATTATTGCTATTCTAGGTTTAGATGAATTATCTGAAGAAGACAGACTTATTGTAGCTCGTGCTCGTAAAAT
TGAACGTTTCTTATCACAACCATTCTTCGTAGCTGAAGTATTTACAGGTTCACCTGGTAAATATGTTTCTTTAGCTGAAA
CTATTGAAGGTTTTGGTAAAATTTTCGCTGGTGAATTAGATGATTTACCAGAACAAGCATTCTACTTAGTAGGTAACATT
ACAGAAGCTATTAGTAAAGCTGCTTCATTAAAATAA

Alignment

ORF - retro_crei_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.33 %
• Parental protein coverage: 75.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GHNVRLVLEVAQHMGDNTVRCVAMDSTDGLVRGQKVVNTGSPIKVPVGRGTLGRIMNVIGEPVDEQGPIE
          G.......EV.Q..GDN.VR.V.M..T.GL.RG..VV.TG.P..VPVG..TLGRI.NV.GEPVD..G...
Retrocopy GTEMAVTCEVQQLLGDNCVRAVSMNPTEGLMRGMEVVDTGKPLSVPVGKVTLGRIFNVLGEPVDNMGNVK

Parental  CSEVWSIHREAPEFTEQSTEQEILVTGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELINNVAKAHGG
          ..E...IHR.AP.F....T...I..TGIKVVDLLAPY.RGGKIGLFGGAGVGKTVLIMELINN.AKAHGG
Retrocopy VEETLPIHRTAPAFVDLDTRLSIFETGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAKAHGG

Parental  FSVFAGVGERTREGNDLYREMIESGVIKLGDKRGESKCTLVYGQMNEPPGARARVALTGLTVAEYFRDVE
          .SVFAGVGERTREGNDLY.EM.ESGVI........SK..LVYGQMNEPPGAR.RVALT.LT.AEYFRDV.
Retrocopy VSVFAGVGERTREGNDLYTEMKESGVI-VEKNLSDSKVALVYGQMNEPPGARMRVALTALTMAEYFRDVN

Parental  GQDVLLFVDNIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGGLQERITTTTKGSITSVQAVYVPADDL
          .QDVL.F.DNIFRF.QA..EVSALLGR.PSAVGYQPTLAT..GGLQERIT.T..GSITS.QAVYVPADDL
Retrocopy KQDVLFFIDNIFRFVQAGAEVSALLGRMPSAVGYQPTLATEMGGLQERITSTKDGSITSIQAVYVPADDL

Parental  TDPAPATTFAHLDATTVLSRSIAELGIYPAVDPLDSTSRMLNPNIIGAEHYNIARGVQKVLQDYKNLQDI
          TDPAPATTFAHLDATTVLSR..A..GIYPAVDPL.STS.ML.P.I.G..HY..A..V.K.LQ.YK.LQDI
Retrocopy TDPAPATTFAHLDATTVLSRNLAAKGIYPAVDPLESTSTMLQPWILGEKHYDSAQSVKKTLQRYKELQDI

Parental  IAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGTPGKYVDLKDTISAFTGILQGKYDDLPEMAF
          IAILG.DELSEED.L.VARARKI.RFLSQPF.VAEVFTG.PGKYV.L..TI..F..I..G..DDLPE.AF
Retrocopy IAILGLDELSEEDRLIVARARKIERFLSQPFFVAEVFTGSPGKYVSLAETIEGFGKIFAGELDDLPEQAF

Parental  YMVGGIHEVVEKADKL
          Y.VG.I.E...KA..L
Retrocopy YLVGNITEAISKAASL

Legend:

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

Expression

RNA-Seq

Chlamydomonas reinhardtii was not studied using RNA-Seq expression data.

ChIP-Seq

Chlamydomonas reinhardtii was not studied using ChIP-Seq data.

EST

Chlamydomonas reinhardtii was not studied using EST data.

TSS

Chlamydomonas reinhardtii was not studied using FANTOM5 data.

Lab

retro_crei_1 was not experimentally validated.

Homology

Retrocopy orthology:

Chlamydomonas reinhardtii 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7,
Arabidopsis thaliana	AT5G08670	1 retrocopy	retro_atha_12,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87,
Brassica rapa	Bra006013	2 retrocopies	retro_brap_51, retro_brap_57,
Chlamydomonas reinhardtii	CHLREDRAFT_78348	1 retrocopy	retro_crei_1 ,
Aegilops tauschii	F775_32946	1 retrocopy	retro_atau_18,
Hordeum vulgare	MLOC_70791	1 retrocopy	retro_hvul_13,
Oryza glaberrima	ORGLA01G0220100	1 retrocopy	retro_ogla_47,
Triticum aestivum	TRAES3BF058700080CFD_g	2 retrocopies	retro_taes_170, retro_taes_31,