RetrogeneDB ID: retro_etel_840

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_173438:2180..2901(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP1
• Ensembl ID: ENSETEG00000014741
• Aliases: None
• Description: poly(rC) binding protein 1 [Source:HGNC Symbol;Acc:8647]

Sequence

>retro_etel_840
GAGAGTACAGGGGCTCAGGTTCAGGTGGCTGGAAATATGCTTCCAATTCAACTGAGCGGGCCATCACTATTGCTGGCATT
CCGCAATCCGTCACTGAGTGTGCCAAGCAGATCTGCGTGGTCATGTTGGAGATGCTCTACCAGTCCCCCCCAAAGGGCAT
GACCATCCCGTACCGGCCCAAGCCGTCCAGTTCTCCGGTCATCCTTGCAGGTGGTCAGGACAGGTAAAGCACAGGAAGCG
ACAGTGCAAGCTTTCCCCATACCACCCTGTCCAGGTGCCTCAACCCTGACCTGGAGGGACCACCTCTAGAGGCCTATACC
ATTCAAGGACAGCATGCCATTCCACAGCCAGATTTGACCAAACTGCACCAGTTGGCAATGCAACAGTCTCATTTTCCTGT
GACGCATGGCAACACCGGATTCAGTGGCATTGAATCCAGCTCTCCAGAGGTGAAAGGCTATTGAGGTTTGGATGCGTCTG
CTCAGACTACTTCTCATGAACTCTCCATTCCAAATGATTTGATTGGCTGCATAATTGGGGGTCAAGGCGCCAAAATCAAT
GAGATCCGTCAGATGTCTGGGGCGCGGATCAAAATCGTGAACCCAGTGGAAGGATCTACTGATAGGCAGGTTACCATCAC
TGGATCTGCTGCCAGCATTAGCCTGGCTCAACATCTAATCAGTGCCAGGCTTTCCTCGGAGACGGTGGCATGGGGAGCAG
C

Alignment

ORF - retro_etel_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.07 %
• Parental protein coverage: 65.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESTGAQVQVAGDMLP-NSTERAITXXXXXXXIIECVKQICVVML----ESPPKGVTIPYRPKPSSSPVIF
          ESTGAQVQVAG.MLP.NSTERAIT.........EC.KQICVVML.....SPPKG.TIPYRPKPSSSPVI.
Retrocopy ESTGAQVQVAGNMLP<NSTERAITIAGIPQSVTECAKQICVVMLEMLYQSPPKGMTIPYRPKPSSSPVIL

Parental  AGGQDRYSTGSDSASFPHTTPSMCLNPDLEGPPLEAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGNT
          AGGQDR.STGSDSASFPHTT.S.CLNPDLEGPPLEAYTIQGQ.AIPQPDLTKLHQLAMQQSHFP.THGNT
Retrocopy AGGQDR*STGSDSASFPHTTLSRCLNPDLEGPPLEAYTIQGQHAIPQPDLTKLHQLAMQQSHFPVTHGNT

Parental  GFSGIESSSPEVKGYWAGLDASAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTD
          GFSGIESSSPEVKGY..GLDASAQTTSHEL.IPNDLIGCIIG.QGAKINEIRQMSGA.IKI.NPVEGSTD
Retrocopy GFSGIESSSPEVKGY-*GLDASAQTTSHELSIPNDLIGCIIGGQGAKINEIRQMSGARIKIVNPVEGSTD

Parental  RQVTITGSAASISLAQYLINVRLSSET-GGMGSS
          RQVTITGSAASISLAQ.LI..RLSSET.GGMGSS
Retrocopy RQVTITGSAASISLAQHLISARLSSET<GGMGSS

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_840 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 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020757	1 retrocopy	retro_btau_175,
Canis familiaris	ENSCAFG00000006821	1 retrocopy	retro_cfam_54,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus	ENSDNOG00000008688	6 retrocopies	retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Echinops telfairi	ENSETEG00000014741	3 retrocopies	retro_etel_1170, retro_etel_2108, retro_etel_840 ,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus	ENSMLUG00000009971	3 retrocopies	retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Mus musculus	ENSMUSG00000056851	1 retrocopy	retro_mmus_274,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92,
Pan troglodytes	ENSPTRG00000005018	1 retrocopy	retro_ptro_113,
Pteropus vampyrus	ENSPVAG00000012284	3 retrocopies	retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,
Ictidomys tridecemlineatus	ENSSTOG00000003635	2 retrocopies	retro_itri_1522, retro_itri_557,