RetrogeneDB ID: retro_ocun_1577

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018701:4635261..4636756(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSOCUG00000013847
• Aliases: None
• Description: t-complex 1 (TCP1), mRNA [Source:RefSeq mRNA;Acc:NM_001163114]

Sequence

>retro_ocun_1577
GACGGGGCCACCATCCTGAAGCTGCTGGAGGTGGAGCATCCCGCAGCCAAAGTGCTCTGTGAGCTGGCCGACCTGCAGGA
TAAGGAAGTTGGAGAGGGAACCGCCTCCATGATCATCATTGCAGCAGAACTGCTAAAGAACGCAGACGAGCTGGTCAAGC
AGAAAATTCACCCCACTTCAGTTATTAGTGGCTACCGGCTTGCTTGCAAGGAAGTAGTGCGCTATATCAGTGAAAACCTG
ATTATTAACACGGATGAACTCGGGAGAGATTGCCTGATGAATGCTGCGAAGACATCAATGTCTTCCAAAATCATCGGAAT
AAATGGAGATTTCTTCTCTAATTTGGTGGAAGATGCTGTGCTTGCTGTTAAATATACAGACGTACGAGGCCAGCCTCGCT
ACCCAGTCAACTCCATCAATATTCTGAAAGCCCACGGGAGAAGCCAGACCGAGAGCATGCTTGTCAGTGGCTATGCTCTC
AACTGTGTGGTGGGATCTCAGGGCATGCCCAAGAGAATAGTTCATGCAAAAATTGCTTGCCTAGACTTCAGCCTGCAAAA
AACAAAAATGAAGCTTGGTGTGCAGGTGGTCATTACAGACCCTGAAAATTGGACCAAGTTAGACAGAGAGAATCAGATAT
GACCAAGGAAAGAATTCAGAAGATCTTGGCCACTGGTGCCGGTGTCATCCTCACCACCGGCGGCATTGATGATTTGTGTC
TCAAGTATTTTGTGGACGCTGGTGCGATGGCAGTTAGGAGAGTTTTAAAGGGGGGTTTTAAGCGAATCGCTAAAGCTTCT
GGAGCAAGTATTCTGTCAACCCTGGCCAACTTGGAAAGTGAAGAGACTTTTGAAGCTGTGATGTTGGGACAAGCAGAGGA
GGTGGTGCAGGAGAGAATCTGTGATGATGAGCTGATCTTAATCACAAACACTAAGGCTGGTACGTCTGCATCCATCATCC
TGCGCGGTGCCAACGGCTTCATGTGTGACAAGATGGAGCGCTCTCTGCATGCTGCTCTCTGAGTGGTGAAGAGAGTTCTG
GAGTCAAAGTCTGTGGCTCCAGGTGGGGGCCCTGTCGAGGCAGCGCTGTCCATGTACCTTGAGAACTAGTCCACCAGCAT
GGGCTCCCAGGAGCAGCTGGCTATTGCAGAGTCCCAGGGTCGCTCCTCGTGATCCCTAGCACGCTGGCCGTGAATGCTGC
CTGGGACTCCACAGATCTGGTTGCAAAGTTGAGAGCTTTTCACAGTGAGGCTCAGGTGAACCCAGAACGGAAAAATCTAA
AATGGATTGGCCTTGCTCTGATCAATGGCAAGCCTCGAGACAACAAGCAGGCAGGGGTGTTTGAACCAACCATAGTGAAA
TAGAGTCTGAAGTTTGCCACAGAGGCTGCAATCACCATTCTCCGGATTGATGACCTCATTAAGTGACGTCCAGAAACTAA
AGATGACAAGCATGGAGGCTACGAAGATGCTGTTCACTCTGGAGCCCTTGATGAC

Alignment

ORF - retro_ocun_1577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.63 %
• Parental protein coverage: 89.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DGATILKLLEVEHPAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACK
          DGATILKLLEVEHPAAKVLCELADLQDKEVG.GT.S..IIAAELLKNADELVKQKIHPTSVISGYRLACK
Retrocopy DGATILKLLEVEHPAAKVLCELADLQDKEVGEGTASMIIIAAELLKNADELVKQKIHPTSVISGYRLACK

Parental  EAVRYISENLIINTDELGRDCLINAAKTSMSSKIIGINGDFFSNMVVDAVLAVKYTDVRGQPRYPVNSIN
          E.VRYISENLIINTDELGRDCL.NAAKTSMSSKIIGINGDFFSN.V.DAVLAVKYTDVRGQPRYPVNSIN
Retrocopy EVVRYISENLIINTDELGRDCLMNAAKTSMSSKIIGINGDFFSNLVEDAVLAVKYTDVRGQPRYPVNSIN

Parental  ILKAHGRSQTESMLVSGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVVITDPE-KLDQIRQ
          ILKAHGRSQTESMLVSGYALNCVVGSQGMPKRIV.AKIACLDFSLQKTKMKLGVQVVITDPE.KLDQ.RQ
Retrocopy ILKAHGRSQTESMLVSGYALNCVVGSQGMPKRIVHAKIACLDFSLQKTKMKLGVQVVITDPE<KLDQVRQ

Parental  RESDITKERIQKILATGANVILTTGGIDDMCLKYFVDAGAMAVRRVLKRDLKRIAKASGASILSTLANLE
          RESD.TKERIQKILATGA.VILTTGGIDD.CLKYFVDAGAMAVRRVLK...KRIAKASGASILSTLANLE
Retrocopy RESDMTKERIQKILATGAGVILTTGGIDDLCLKYFVDAGAMAVRRVLKGGFKRIAKASGASILSTLANLE

Parental  GEETFEAVMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLES
          .EETFEAVMLGQAEEVVQERICDDELILI.NTKA.TSASIILRGAN.FMCD.MERSLH.AL.VVKRVLES
Retrocopy SEETFEAVMLGQAEEVVQERICDDELILITNTKAGTSASIILRGANGFMCDKMERSLHAAL*VVKRVLES

Parental  KSVVPGGGAVEAALSIYLENYATSMGSREQLAIAE-FARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEA
          KSV.PGGG.VEAALS.YLEN..TSMGS.EQLAIAE....SLLVIP.TLAVNAA.DSTDLVAKLRAFH.EA
Retrocopy KSVAPGGGPVEAALSMYLEN*STSMGSQEQLAIAE<VPGSLLVIPSTLAVNAAWDSTDLVAKLRAFHSEA

Parental  QVNPERKNLKWIGLDLINGKPRDNKQAGVFEPTIVKVKSLKFATEAAITILRIDDLIKLHPETKDDKHGG
          QVNPERKNLKWIGL.LINGKPRDNKQAGVFEPTIVK..SLKFATEAAITILRIDDLIK..PETKDDKHGG
Retrocopy QVNPERKNLKWIGLALINGKPRDNKQAGVFEPTIVK-*SLKFATEAAITILRIDDLIK*RPETKDDKHGG

Parental  YEDAVHSGALDD
          YEDAVHSGALDD
Retrocopy YEDAVHSGALDD

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.06 RPM	182.23 RPM
SRP017611_kidney	0.00 RPM	178.39 RPM
SRP017611_liver	0.00 RPM	93.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1577 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1577 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577 ,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Rattus norvegicus	ENSRNOG00000014160	1 retrocopy	retro_rnor_2091,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,