RetrogeneDB ID: retro_etel_1015

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_200740:12338..13084(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSETEG00000016984
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]

Sequence

>retro_etel_1015
ATGGTGAAAGACACCACTGATGTTTTGGGGGTCAAACCCAGTGCCACCCAGGAAGAGCTGAAAAAAGCTTACCGGAAACT
GGCCTTGAAGTACCATCCTGATAAGAATCCAAGTGAAGGCGAGAAGTTTAAACAGATTTCTCAAGCATATGAGGTGCTTT
CTGATGCCAAGAAAAGAGAATTGTATGACAAAGGAGGCGAGCAGGCCATCAAGGAGCGTGGAGCAGGCGGTGGATTTGGT
TCCCGATGGACATCTTTGATATGTTCTTTGGAGGCGGCGGACGGATGCAGAGAGAAAGGAGAGGAAAAAACGTGGTGCAC
CAACTCTCAGTAACATTAGAAGATTTGTATAATGGTGCAACAAGAAAACTGGCCCTGCAAAAGAATGTGATTTGTGACAA
ATGTGAAGGCCGAGGCGGTAAGAAAGGAGCCATAGAGTGCTGTCCTAACTGCCGTGGTACTGGGATGCAGATACGAATCC
ATCAGATAGGGCCTGGAATGGTGCAGCAAATTCAGTCTGTGTGCATGGAGTGCCAGGGCCAGGGGGAACAGATCAGCCCT
AAAGACAAATGTAAAAGTTGCAATGGAAGGAAGATCGTTCGTGAGAAGATTCTAGAAGTTCATATTGACAAAGGCATGAA
AGACGGCCAGAAGATCACATTCCACGGTGAAGGAGACCAAGAGCCTGGACTGGAGCCAGGAGATATTATTCTTGTTTTAG
ATCAGAAGGACCATGCTGTTTTTACC

Alignment

ORF - retro_etel_1015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.07 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVKETTYYDVLGVKPSATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGEQ
          MVK.TT..DVLGVKPSATQEELKKAYRKLALKYHPDKNP.EGEKFKQISQAYEVLSDAKKRELYDKGGEQ
Retrocopy MVKDTT--DVLGVKPSATQEELKKAYRKLALKYHPDKNPSEGEKFKQISQAYEVLSDAKKRELYDKGGEQ

Parental  AIKEGGAGGGFGS-PMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEG
          AIKE.GAGGGFGS.PMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEG
Retrocopy AIKERGAGGGFGS<PMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEG

Parental  RGGKKGAV-CCPNCRGTGMPIRIHQIGPGMVQQIKSVCMECQGHGERISPKDRCKSCNGRKIVREKKILE
          RGGKKGA..CCPNCRGTGM.IRIHQIGPGMVQQI.SVCMECQG.GE.ISPKD.CKSCNGRKIVRE.KILE
Retrocopy RGGKKGAIECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGQGEQISPKDKCKSCNGRKIVRE-KILE

Parental  VHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFT
          VHIDKGMKDGQKITFHGEGDQEPGLEPGDII.VLDQKDHAVFT
Retrocopy VHIDKGMKDGQKITFHGEGDQEPGLEPGDIILVLDQKDHAVFT

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_1015 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 8 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Echinops telfairi	ENSETEG00000016984	6 retrocopies	retro_etel_1015 , retro_etel_1454, retro_etel_1751, retro_etel_219, retro_etel_482, retro_etel_623,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mustela putorius furo	ENSMPUG00000004231	2 retrocopies	retro_mputfur_1543, retro_mputfur_487,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,