RetrogeneDB ID: retro_rnor_2091

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:185422158..185423451(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tcp1
• Ensembl ID: ENSRNOG00000014160
• Aliases: Tcp1, CCTalpha, Tcp-1
• Description: T-complex protein 1 subunit alpha [Source:UniProtKB/Swiss-Prot;Acc:P28480]

Sequence

>retro_rnor_2091
AGGGAAGCAGTGCGATATATCAATGAGAACCTAATTATCAACACAGACGAACTTGGAAGAGACTGTCTGATCAATGCTGC
TAAGACATCCATGTCTTCCAAAATTATTGGAATAAATGGTGATTTCTTCGCTAATATGGTGGTAGACGCTGTGCTTGCTG
TTAAATACACAGATATACGAGGCCAGCCTCGCTATCCAGTCAATTCTGTTAATATTCTAAAAGCCCACGGGAGAAGTCAG
ATAGAAAGCATGCTGATCAATGGCTATGCACTCAACTGTGTGGTTGGATCTCAGGGCATGCTCAAGAGAATAGTTAATGC
AAAAATTGCTTGTCTTGACTTCAGCCTGCAGAAAACAAAAATGAAGCTTGGTGTACAAGTGGTTATTACAGACCCTGAGA
AACTGGACCAGATTAGACAGAGAGAATCCGATATCACCAAGGAGAGAATTCAGAAGATCCTGGCAACTGGTGCCAACGTT
ATTCTAACCACCGGTGGGATTGATGACATGTGTCTGAAGTATTTTGTGGAAGCTGGTGCCATGGCTGTTAGGAGAGTTTT
AAAAAGAGACCTCAAACGTATTGCAAAAGCTTCTGGAGCAAGTATCCTGTCTACACTGGCCAATTTGGAAGGTGAAGAGA
CTTTTGAGGCAACAATGTTGGGACAAGCGGAAGAGGTCGTACAGGAGAGGATTTGTGACGATGAGCTGATCTTAATCAAA
AATACTAAGGCTCGTACGTCAGCTTCAATTATCTTACGAGGAGCAAACGACTTCATGTGTGATGAAATGGAACGCTCCTT
ACATGACGCTCTTTGTGTGCTGAAGGGAGTTTTGGAGTCAAAGTCTGTGGTCCCAGGTGGAGGTGCTGTAGAAGCGGCCT
TGTCTATATACCTTGAAAACTATGCGACCAGTATGGGATCTCGGGAACAGCTTGCTATTGCAGAGTTTGCAAGATCTCTG
CTTGTGATTCCTAATACACTGGCAGTGAATGCTGCCCAAGACTCCACTGACCTGGTTGCCAAGTTAAGAGCTTTTCACAA
TGAGGCTCAAGTTAACCCAGAACGTAAAAATCTAAAGTGGATTGGTCTTGATTTGGTCCATGGGAAACCACGAGACAATA
AGCAAGCGGGGGTGTTTGAACCAACCATAGTTAAAGTAAAGAGCCTGAAGTTTGCAACAGAGGCTGCAATCACCATACTT
CGGATTGATGATCTGATAAAATTACACCCAGAAAGCAAAGACGACAAACACGGAGGTTATGAAAATGCTGTTCACTCTGG
AGCCCTTGATGAC

Alignment

ORF - retro_rnor_2091 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.3 %
• Parental protein coverage: 77.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEAVRYINENLIINTDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAVKYTDIRGQPRYPVNSV
          .EAVRYINENLIINTDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAVKYTDIRGQPRYPVNSV
Retrocopy REAVRYINENLIINTDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAVKYTDIRGQPRYPVNSV

Parental  NILKAHGRSQIESMLINGYALNCVVGSQGMLKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQ
          NILKAHGRSQIESMLINGYALNCVVGSQGMLKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQ
Retrocopy NILKAHGRSQIESMLINGYALNCVVGSQGMLKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQ

Parental  RESDITKERIQKILATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGASILSTLANLE
          RESDITKERIQKILATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGASILSTLANLE
Retrocopy RESDITKERIQKILATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGASILSTLANLE

Parental  GEETFEATMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLES
          GEETFEATMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCV.K.VLES
Retrocopy GEETFEATMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVLKGVLES

Parental  KSVVPGGGAVEAALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEAQ
          KSVVPGGGAVEAALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEAQ
Retrocopy KSVVPGGGAVEAALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEAQ

Parental  VNPERKNLKWIGLDLVHGKPRDNKQAGVFEPTIVKVKSLKFATEAAITILRIDDLIKLHPESKDDKHGGY
          VNPERKNLKWIGLDLVHGKPRDNKQAGVFEPTIVKVKSLKFATEAAITILRIDDLIKLHPESKDDKHGGY
Retrocopy VNPERKNLKWIGLDLVHGKPRDNKQAGVFEPTIVKVKSLKFATEAAITILRIDDLIKLHPESKDDKHGGY

Parental  ENAVHSGALDD
          ENAVHSGALDD
Retrocopy ENAVHSGALDD

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	0.79 RPM	46.59 RPM
SRP017611_kidney	0.28 RPM	62.32 RPM
SRP017611_liver	0.00 RPM	44.85 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2091 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2091 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
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,