RetrogeneDB ID: retro_etel_1493

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_274210:1036..1403(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIB
• Ensembl ID: ENSETEG00000012671
• Aliases: None
• Description: peptidylprolyl isomerase B (cyclophilin B) [Source:HGNC Symbol;Acc:9255]

Sequence

>retro_etel_1493
GGATACAAAGGAAACACCTTCCACAGGGTCATAAAGGATTTCATGATCCAGGGTGGAGATTTTATAAAAGGAGATGGTAC
TGGAGTTGCCAGTATTTACCGAGGACCACTTGCAGATGAAAATGTTAAACTCAGATATTCAGCTCCAGGTCTGCTTTCCA
TGGCAGACAGTGGTCCCAGTACAAATGGCTGCTGGTTTTTCATCACCTGTTCTAAATGTGATGGGCTGGATGAGAAGCAC
GCGGTGTTTGGAAAAATCATCGGTGGACTTCTGGTGATGAGAAAAATTGAGAAAGTTCCCATGGGGTGCCAACAATAAGC
CCAAGCTGCCTGTGGAGATCTCACAGTATGGAGAGATGTAAATGGAA

Alignment

ORF - retro_etel_1493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.03 %
• Parental protein coverage: 71.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYKDSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGERFPDENFKLKHYGPGWVSMANAGKDTNGSQFFITT
          GYK...FHRVIKDFMIQGGDF..GDGTG..SIY.....DEN.KL....PG..SMA..G..TNG..FFIT.
Retrocopy GYKGNTFHRVIKDFMIQGGDFIKGDGTGVASIYRGPLADENVKLRYSAPGLLSMADSGPSTNGCWFFITC

Parental  VKTSWLDGKHVVFGKVLEGMDVVRKVESTKT-DGRDKPLKDVTIADCGKIEVE
          .K...LD.KH.VFGK...G..V.RK.E.........KP...V.I...G....E
Retrocopy SKCDGLDEKHAVFGKIIGGLLVMRKIEKVPM>GANNKPKLPVEISQYGEM*ME

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_1493 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017053	1 retrocopy	retro_cfam_1999,
Equus caballus	ENSECAG00000017164	1 retrocopy	retro_ecab_617,
Echinops telfairi	ENSETEG00000012671	1 retrocopy	retro_etel_1493 ,
Loxodonta africana	ENSLAFG00000018698	1 retrocopy	retro_lafr_521,
Oryctolagus cuniculus	ENSOCUG00000012012	1 retrocopy	retro_ocun_413,