RetrogeneDB ID: retro_etel_1901

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_312527:162010..162399(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSETEG00000007481
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_etel_1901
ATGAATGGCACAGGCACTATCCGGACCAGGGAGTTCATGACCAACTGACGACTTCAGTGAAAACCAAGGGTCATCGATGC
CCCTCGCCCTGGGAAAGGGACAGTGCCCGAGACAGAAATGTGTGAAAAAAACTAGCCAAAATGTGCAAGACCATACCAGA
CGTCATTTTTGTATTTGGCTTTAGAACCCACTTGGTGGTGGCAAGACTACTGACTTTGGCATGGTTTACGATTCCTTGGA
CGATGCAGAGAAAAGTGAGCCTGCACACAGACTTGCCAGACCGGCCTGCGTGAGAAGAAAAGGCGCTCAGAGAAGAGCGG
GAGGACCGCAAGAACCAATGAAGACGGGCCCGGGGCTGCCAAGGCCAGCACTGGGGCGGCAAAAATAAA

Alignment

ORF - retro_etel_1901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.78 %
• Parental protein coverage: 98.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPG-KATVPKTE-IREKLAKMYKTTPDVIFVFGFRTH-FGGG
          MN.T.TIRTR.FMTN..LQ.K..VID...PG.K...P.......KLAKM.KT.PDVIFVFGFRTH..GGG
Retrocopy MNGTGTIRTREFMTN*RLQ*KPRVIDAPRPG>KGQCPRQK>V*KKLAKMCKTIPDVIFVFGFRTH<LGGG

Parental  KTTGFGMIYDSL-DYKKNEPKHRLAR-HGLYEKKKTS-RKQRKERKNRMKKVRGTAKANVGAGKK
          KTT.FGM.YDSL.D..K.EP.HRLAR..GL.EKK..S.R..R..RKN.....RG......G...K
Retrocopy KTTDFGMVYDSLDDAEKSEPAHRLAR<TGLREKKRRS<REEREDRKNQ*RRARGCQGQHWGGKNK

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_1901 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 7 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010243	18 retrocopies	retro_dnov_1299, retro_dnov_1305, retro_dnov_1394, retro_dnov_1444, retro_dnov_1470, retro_dnov_1471, retro_dnov_168, retro_dnov_1889, retro_dnov_1920, retro_dnov_1985, retro_dnov_2074, retro_dnov_2357, retro_dnov_288, retro_dnov_309, retro_dnov_551, retro_dnov_73, retro_dnov_782, retro_dnov_92,
Echinops telfairi	ENSETEG00000007481	32 retrocopies	retro_etel_1119, retro_etel_1242, retro_etel_1274, retro_etel_1339, retro_etel_1395, retro_etel_1663, retro_etel_1688, retro_etel_1783, retro_etel_1800, retro_etel_1806, retro_etel_183, retro_etel_1901 , retro_etel_1934, retro_etel_1978, retro_etel_1991, retro_etel_2040, retro_etel_2104, retro_etel_223, retro_etel_287, retro_etel_289, retro_etel_369, retro_etel_422, retro_etel_476, retro_etel_503, retro_etel_523, retro_etel_67, retro_etel_744, retro_etel_752, retro_etel_815, retro_etel_904, retro_etel_91, retro_etel_94,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Monodelphis domestica	ENSMODG00000025091	3 retrocopies	retro_mdom_1303, retro_mdom_1706, retro_mdom_1914,
Ornithorhynchus anatinus	ENSOANG00000006329	1 retrocopy	retro_oana_54,
Sarcophilus harrisii	ENSSHAG00000008090	3 retrocopies	retro_shar_276, retro_shar_303, retro_shar_697,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289, retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,