RetrogeneDB ID: retro_etel_312

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_5144:122576..123202(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA4
• Ensembl ID: ENSETEG00000002722
• Aliases: None
• Description: developmental pluripotency associated 4 [Source:HGNC Symbol;Acc:19200]

Sequence

>retro_etel_312
CAAAACAGTGCGTCTCAAGTGACTACACAGAAAAGAATTAAAAAAGAACAAGATAATTAGCCAAGCGATGACAGCTTGAA
ACCCCGACAGAAGATTCCGATTCCTCCATTACCATCAAAACTGCCACCAGTCCACCCGGTTCACCGAGACATCCTGCGGG
CCTGGTGCCATCAATTTAAGCTGAGCACCAAAGGCCAGAAACTAGATGCATATAGCGGCTGTGTGAACGTGCTTCCCCAA
GTCAAACTCAGAATTTTCCTGCCACAGCAAAGGAAGCCAAGATCCAGGCACGGCTAAAAAAATCAAATGTGACCAAATCA
AATCTAGATGGTTCGCAGAAAAAGAACATGTGTCCTGAAGGGACTGACCCTCCTGAAGTGGCTCCTTCCTCTGAAGAAGG
GGCGCCTGCCTTTGAATCTGTTCTCCAGCAGGATGTCAATGCAGTTGGCAATACAGTATGACAGGTGACAAGCTCCACAG
GGAGGCTGTGCTGGCAGGTGGAGGTAGACGAATCACAAGAGACGTATGCTTTCAGGTGGTATGTGGCACGTGGGAGAAGT
CTCCCTGCAAACAGAAGTGGCTGGGTTCGGTTGCAGTTTCGTGCTGGACAAGCCTGGGTCCGAGAA

Alignment

ORF - retro_etel_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.48 %
• Parental protein coverage: 79.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGSSTEKPAEESFPKESSQ--SDDNLKPRKKIPIPPLPSKLPPVHLVHRDILRAWCHQLKLSTKGQKLDA
          ..S...........KE.....SDD.LKPR.KIPIPPLPSKLPPVH.VHRDILRAWCHQ.KLSTKGQKLDA
Retrocopy QNSASQVTTQKRIKKEQDN*PSDDSLKPRQKIPIPPLPSKLPPVHPVHRDILRAWCHQFKLSTKGQKLDA

Parental  YK-RLCEYRFPSQ-KNFPATAKEAKIQTRLKKSNVVKQKMNMCPEGTKPPEAAPSSAEGAPAFESVLQQD
          Y..RLCE...PSQ..NFPATAKEAKIQ.RLKKSNV.K............PE......E.AP..E......
Retrocopy YS<RLCERASPSQTQNFPATAKEAKIQARLKKSNVTKSNLDGSQKKNMCPEGT-DPPEVAPSSE----EG

Parental  SNAVDNTVIQVTSSTSEAVLASWSRIAGKAGKVEVEESPQETYAVRWCVVHGRSLPANRSGWVRLQFHAG
          ..A......Q........V....S........VEV.ES.QETYA.RW.V..GRSLPANRSGWVRLQF.AG
Retrocopy APAFESVLQQDVNAVGNTV*QVTSSTGRLCWQVEVDES-QETYAFRWYVARGRSLPANRSGWVRLQFRAG

Parental  QAWVPE
          QAWV.E
Retrocopy QAWVRE

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_312 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 20 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010335	5 retrocopies	retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus	ENSCJAG00000020171	2 retrocopies	retro_cjac_1334, retro_cjac_1491,
Echinops telfairi	ENSETEG00000002722	1 retrocopy	retro_etel_312 ,
Echinops telfairi	ENSETEG00000007985	4 retrocopies	retro_etel_2051, retro_etel_2058, retro_etel_506, retro_etel_918,
Homo sapiens	ENSG00000121570	1 retrocopy	retro_hsap_893,
Gorilla gorilla	ENSGGOG00000015121	2 retrocopies	retro_ggor_1970, retro_ggor_723,
Loxodonta africana	ENSLAFG00000016804	1 retrocopy	retro_lafr_456,
Myotis lucifugus	ENSMLUG00000016423	1 retrocopy	retro_mluc_973,
Macaca mulatta	ENSMMUG00000016901	1 retrocopy	retro_mmul_1515,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mustela putorius furo	ENSMPUG00000010206	1 retrocopy	retro_mputfur_800,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Nomascus leucogenys	ENSNLEG00000004030	3 retrocopies	retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus	ENSOCUG00000016435	1 retrocopy	retro_ocun_114,
Pongo abelii	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus	ENSPVAG00000010677	1 retrocopy	retro_pvam_1237,
Rattus norvegicus	ENSRNOG00000025404	4 retrocopies	retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tursiops truncatus	ENSTTRG00000009508	1 retrocopy	retro_ttru_1772,