RetrogeneDB ID: retro_etel_1010

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_200085:5009..5865(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA4
• Ensembl ID: ENSETEG00000004320
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:HGNC Symbol;Acc:14885]

Sequence

>retro_etel_1010
AAACAGATTTTTCAAGCATTTAAAGTGTTTTCTGATGCAAAGAAAATAGAATTATATGACATTGGAGGTGAGCAAGCCAT
CAAGGAGGGTGGACAGGTGGTGTGTTTTTGTTCTCCAATGGACATCTTTGATATGTTCTTTGGAGGTGGTGGAAGGGTCC
CGAGAGAAAGGACAGGAAAAAATGTTGTGCATCAAATCTCACTAACATTAGAAGATATGTATAATGGCGCAATAAGAAAA
CTAACTCTGCAAAAGAATGTGATTTGTAAAAAATGTGAAGGCCGAGGTGGTAAGAAAGAAGCAGTAGAATGCTGTCCTAA
CTGCTGAGGTACTTGAATACAAATATGAATTCATCAGATAGGACCTGGAATAGTTCAGCAAATTCAGTCTCTGTGCATAG
AGTGCAAGGGCCATGGGGAACCAATCAGCCCTAAAGATAGACATGAAAGTTGCAATGGAAGGAAGATAGTTCATGAGAAG
AAGATTCTATAAGTTCACATTAACAAAGGTATGAAAGATGGGCAGAAGATAACATTCCATATTGGAATAGACCAAGAACC
TGGACTGGAGTCAGGAGATATGATTACTATTTTAGATCAGAAGGACCATTCTGTTTTTACCAAATGAGGAGAAGACCTTT
TCACGAGTATGGACACACAGCTGGTTGAAGCGTTGTGTGTGTTCCAAAATACAGTATCTACTCTAGACAACCGATCCATA
GTCATCACTTCTCACCCAGGTCAGAATGTGCAGCATACATATATTAAATATGTGCTACATGAAGGCATTTTAGTTTATTG
CAGACCTGATGAAAAGGGGTGTCTAATGCGTTGAATTTAAGGTGAACTTCCCCGAG

Alignment

ORF - retro_etel_1010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.37 %
• Parental protein coverage: 81.02 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLISQAYEVLSDPKKRDIYDQGGEQAIKEGGSGSPNFSSPMDIFDMFFGGGGRMARERRGKNVVHQLSVT
          K.I.QA..V.SD.KK...YD.GGEQAIKEGG.....F.SPMDIFDMFFGGGGR..RER.GKNVVHQ.S.T
Retrocopy KQIFQAFKVFSDAKKIELYDIGGEQAIKEGGQ-VVCFCSPMDIFDMFFGGGGRVPRERTGKNVVHQISLT

Parental  LEDLYNGVTKKLALQKNVICEKCEGVGGKKGSVEKCPLCKGRGMQIHIQQIGPGMVQQIQTVCIECKGQG
          LED.YNG...KL.LQKNVIC.KCEG.GGKK..VE.CP.C.G...QI.I.QIGPG.VQQIQ..CIECKG.G
Retrocopy LEDMYNGAIRKLTLQKNVICKKCEGRGGKKEAVECCPNC*GT*IQI*IHQIGPGIVQQIQSLCIECKGHG

Parental  ERINPRDRCEGCSGAKVVREKKLIEVHVEKGMKDGQKILFHGEGDQEPELEPGDVIIVLDQKDHSVFQRQ
          E.I.P.DR.E.C.G.K.V.EKK...VH..KGMKDGQKI.FH...DQEP.LE.GD.I..LDQKDHSVF...
Retrocopy EPISPKDRHESCNGRKIVHEKKIL*VHINKGMKDGQKITFHIGIDQEPGLESGDMITILDQKDHSVFTK*

Parental  GHDLIVKMKIQLSEALCGFKKTISTLDDRTLVIASKSGEVIKHGDLKCVRNEGMPIYKAPLEKGTLI-IQ
          G.DL...M..QL.EALC.F..T.STLD.R..VI.S..G....H...K.V..EG...Y..P.EKG.L....
Retrocopy GEDLFTSMDTQLVEALCVFQNTVSTLDNRSIVITSHPGQNVQHTYIKYVLHEGILVYCRPDEKGCLM>VE

Parental  FLVLFPE
          F.V.FPE
Retrocopy FKVNFPE

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_1010 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 11 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333, retro_dord_533,
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,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292, retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760, retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276, retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752,