RetrogeneDB ID: retro_sara_624

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_243479:4555..5404(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSSARG00000002463
• Aliases: None
• Description: t-complex 1 [Source:HGNC Symbol;Acc:11655]

Sequence

>retro_sara_624
CGAATTCAGAAGATCCTGGCAACGGGGGCCAATGTCATCCTCACCACTGGTGGCATTGATGACATGTGTCTGAAGTATTT
TGTGGAGTCTGGCTCCATGGCAGTCAGGAGAGTCTTGAAAAGGGACCTGAAGCGCATCGCTAAAGCGTCTGGAGCGGTGA
TTCTGTCAACCTTGGCCAATTTGGAAGGTGAAGAAACTTTTGAATCTTCCATGTTGGGACAAGCGGAAGAGGTGGTACAG
GAGAGAATCTGTGATGACGAGCTGATTTTGATCAAGAACACTAAGGCTCGCTCCTCGGCATCCATTATCCTACGTGGGGC
GAACGATTTCATGTGTGACGAGATGGAGCGCTCCTTACATGACGCGCTGTGTGTGGTGAAGAGAGTGCTGGAGTCCAAGT
CTGTGGTTCCTGGTGGGGGCGCGGTGGAATCCGCCCTGTCCATCTACCTGGAGAACTACGCCACCAGTATGGGATCTCGG
GAACAACTAGCTATCGCAGAATTTGCGAGATCTCTTCTAGTTATTCCAAACACTTTGGCGGTCAACGCAGCTCAAGATTC
TACAGATCTAGTTGCAAAGCTGAGAGCCTTCCATAATGAGGCCCAAGTCAACCCAGAGCGCAAAAACCTGAAATGGATTG
GTCTTGATTTGGTCAATGGTAAGCCTCGTGACAACAAGCAAGCCGGTGTGTTTGAACCAACCATAGTTAAGATAAAGAGT
TTGAAGTTTGCAACAGAAGCTGCTATTACCATTCTTCGGATTGATGATCTGATTAAATTACACCCAGAAAGCAAAGAGGA
TAAGCATGGAGGTTACGAAGATGCCGTCCACTCGGGCGCCCTTGATGAC

Alignment

ORF - retro_sara_624 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.94 %
• Parental protein coverage: 51.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RIQKILATGPNVILTTGGIDDMCLKY-VESGSMAVRRVLKRDLKRIAKASGAVILSTLANLEGEETFESS
          RIQKILATG.NVILTTGGIDDMCLKY.VESGSMAVRRVLKRDLKRIAKASGAVILSTLANLEGEETFESS
Retrocopy RIQKILATGANVILTTGGIDDMCLKYFVESGSMAVRRVLKRDLKRIAKASGAVILSTLANLEGEETFESS

Parental  MLGQAEEVVQERICDDELILIKNTKARSSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGG
          MLGQAEEVVQERICDDELILIKNTKARSSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGG
Retrocopy MLGQAEEVVQERICDDELILIKNTKARSSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGG

Parental  AVEAALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEAQVNPERKNL
          AVE.ALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEAQVNPERKNL
Retrocopy AVESALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEAQVNPERKNL

Parental  KWIGLDLVNGKPRDNKQAGVFEPTIVKIKSLKFATEAAITILRIDDLIKLHPESKEDKHGGYEDAVHSGA
          KWIGLDLVNGKPRDNKQAGVFEPTIVKIKSLKFATEAAITILRIDDLIKLHPESKEDKHGGYEDAVHSGA
Retrocopy KWIGLDLVNGKPRDNKQAGVFEPTIVKIKSLKFATEAAITILRIDDLIKLHPESKEDKHGGYEDAVHSGA

Parental  LDD
          LDD
Retrocopy LDD

Legend:

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

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_624 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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 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,