RetrogeneDB ID: retro_etel_1640

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_284750:38474..38752(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP2
• Ensembl ID: ENSETEG00000010240
• Aliases: None
• Description: ribosomal protein, large, P2 [Source:HGNC Symbol;Acc:10377]

Sequence

>retro_etel_1640
ATGCGCCACGTCGCCTCCTACCTGCTGGCTGCTCTGAGGGCAATGCGTCTCCCAGCGCCAAGGACAGCAAGAGAATCCTG
GACAGCGGCGACGACAAGCGACTCAACAAGGTCATCAAGGAGTTTGGGACTTGGGACGGGAAGATCACTGCAGACGCCGT
TGGCCAGGGGATTGGCAAGCTCGCCCGTGTGCCTGCGGGCGGCGCTGTGGCCGTCCTGGGCTCGGCCCCACCTGCGGAGC
AGAAAGAGCAGGAGGGGGAGGAGTCCAAGGAGTCGGAA

Alignment

ORF - retro_etel_1640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.4 %
• Parental protein coverage: 84.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRYVASYLLAALG-GNASPSAKDIKKILDSVGIEADDDRLNKVISEL---NGKNIEDVIAQGIGKLASVP
          MR.VASYLLAAL..GNASPSAKD.K.ILDS.....DD.RLNKVI.E.....GK...D...QGIGKLA.VP
Retrocopy MRHVASYLLAALR<GNASPSAKDSKRILDS----GDDKRLNKVIKEFGTWDGKITADAVGQGIGKLARVP

Parental  AGGAVAVSAAPGSAAPAAGSAPAAAEEKKDE
          AGGAVAV....GSA.PA........E.K..E
Retrocopy AGGAVAVL---GSAPPAEQKEQEGEESKESE

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1640 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006935	1 retrocopy	retro_amel_197,
Bos taurus	ENSBTAG00000001777	2 retrocopies	retro_btau_117, retro_btau_1399,
Canis familiaris	ENSCAFG00000009523	1 retrocopy	retro_cfam_18,
Ciona intestinalis	ENSCING00000000626	1 retrocopy	retro_cint_34,
Callithrix jacchus	ENSCJAG00000011838	6 retrocopies	retro_cjac_2399, retro_cjac_2497, retro_cjac_2539, retro_cjac_2745, retro_cjac_3097, retro_cjac_3859,
Echinops telfairi	ENSETEG00000010240	4 retrocopies	retro_etel_1206, retro_etel_1458, retro_etel_1640 , retro_etel_455,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Macaca mulatta	ENSMMUG00000020627	2 retrocopies	retro_mmul_221, retro_mmul_311,
Mustela putorius furo	ENSMPUG00000009049	1 retrocopy	retro_mputfur_254,
Nomascus leucogenys	ENSNLEG00000026860	5 retrocopies	retro_nleu_1948, retro_nleu_2144, retro_nleu_2296, retro_nleu_2762, retro_nleu_85,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Rattus norvegicus	ENSRNOG00000002116	3 retrocopies	retro_rnor_257, retro_rnor_320, retro_rnor_388,
Sarcophilus harrisii	ENSSHAG00000001056	1 retrocopy	retro_shar_321,
Sus scrofa	ENSSSCG00000012842	1 retrocopy	retro_sscr_54,