RetrogeneDB ID: retro_tbel_3323

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_137290:97472..98423(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP0
• Ensembl ID: ENSTBEG00000005498
• Aliases: None
• Description: ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]

Sequence

>retro_tbel_3323
ATGCCCAGGGAAGACAGGGCGACCTGGAAGTCCAACTACTTCCTTAAGATCATCCAACTTCTGGATGATTATCCAAAATG
CTTCGTTGTGGGTGCAGACAATGTGGGCTCCAGGCAGATGCAGCAGATCCGCATGTCCCTCCGCAGGAAGGCCGTGGTGC
TGATGGGCAAGATCACCATGATGCGCAAGGCCATCCAGGGGCATCTGGAAAACAACCCAGCTCTGGAGAAGCTGTTGCCT
CACATCCAGGGGAATGTGGGCTTCATGTTCACCAAGGAGGACCTCACTGAGATCAGGGACATGTTGCTGGCCAACACGGT
TCCAGCTGCTGCCCATGCTGGTGCCATTGCCCCTTGCGAAGTCAATGTGCCAGCCCAGACCACTGGTCTGGGGCCCGAGA
AGACCTCCTTCTTCCAGGCTTTGGGCATCACCGCTAAGATTTCCAGGGGCACCATTGAAATCCTGAGCAATGTGCAGCTG
ATAAAGACTGGAGACAAGGTGGGAGCCAGAGAAGCCACACTGCTGAACATGCTGAACATCTCCCCCTTCTCCTTCGGGCT
GATCATCCAGCAGGTGTTTGACAACGGCAGCATCTACAACCCCGAAGTGCTTGACATCACAGAGGAGGCTCTGCATTCTC
GCTTCCTGGAGGGTGTCCGCAATGTTGCCAGTGTGTGCCTGCAAATTGGCTATCCCACTGTCGCTTCAGTGCCACATTCT
ATCATCAATGGGTACAAGCAGGTCCTGGCTTTGTCTGTGGAGACTGACTACACCTTCCCACTTGCCGAGAAAGTCAAGGC
CTTCTTGGCTGATCCATCTGCATTTATGGCTGCCGCCCCCGTGGCTGCTGCCACCACTGCTGCTCCTGCTGCTGCTGCAG
CCCCAGCCAAGGTTGAAGCCAAGGAAGAGTCGGAGGAGTCAGACGAAGATATGGGATTTGGTCTCTTTGAC

Alignment

ORF - retro_tbel_3323 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE
          MPREDRATWKSNYFLKIIQLLDDYPKCF.VGADNVGS.QMQQIRMSLR.KAVVLMGK.TMMRKAI.GHLE
Retrocopy MPREDRATWKSNYFLKIIQLLDDYPKCFVVGADNVGSRQMQQIRMSLRRKAVVLMGKITMMRKAIQGHLE

Parental  NNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQA
          NNPALEKLLPHI.GNVGF.FTKEDLTEIRDMLLAN.VPAAA.AGAIAPCEV.VPAQ.TGLGPEKTSFFQA
Retrocopy NNPALEKLLPHIQGNVGFMFTKEDLTEIRDMLLANTVPAAAHAGAIAPCEVNVPAQTTGLGPEKTSFFQA

Parental  LGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEEA
          LGIT.KISRGTIEILS.VQLIKTGDKVGA.EATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEEA
Retrocopy LGITAKISRGTIEILSNVQLIKTGDKVGAREATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEEA

Parental  LHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAAP
          LHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYK.VLALSVETDYTFPLAEKVKAFLADPSAF.AAAP
Retrocopy LHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKQVLALSVETDYTFPLAEKVKAFLADPSAFMAAAP

Parental  VAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD
          V............APAKVEAKEESEESDEDMGFGLFD
Retrocopy VXXXXXXXXXXXXAPAKVEAKEESEESDEDMGFGLFD

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3323 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3323 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 14 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002745	2 retrocopies	retro_chof_1115, retro_chof_2341,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus	ENSCPOG00000021812	5 retrocopies	retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Erinaceus europaeus	ENSEEUG00000007553	1 retrocopy	retro_eeur_612,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,
Tupaia belangeri	ENSTBEG00000005498	1 retrocopy	retro_tbel_3323 ,