RetrogeneDB ID: retro_etel_1124

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_215346:2369..3095(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000017307
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TOMM40L
• Ensembl ID: ENSETEG00000015755
• Aliases: None
• Description: translocase of outer mitochondrial membrane 40 homolog (yeast)-like [Source:HGNC Symbol;Acc:25756]

Sequence

>retro_etel_1124
GGGCTGTGCCCCACCAGGAGCTCTGCCCAGCCCTGGGATCCTCTTCCTAACTCTGGGAGCTTCAATGCGCTACATGGAAT
ATGCAAAGAGGTATCTCTAGCCCAGACAGAAGGAGTGAAGCTCATTGTCAACAAGATTCTGAGCAGCCATTTCCAAGTGG
TGCACACTGTGAATATGAAGGCCCTGAGCTATCACCTCCACGCCATCCATGCTGGGGACTGTCCGCTTAGCCCCAGTGAG
GTGTTCCCCATTGTGGTCAGGAACATGGACAGCAGTGGCAGCCTCAATGCCCGAGTCCTACTCCTCTTGGCAGAGCGGCT
TCGAGCTAAGGTTGTCTTCCAGATGCATCAGGCCAAGTTCCAGATGTGGCAGTTTGATAGTGAGTATCGGGGAGATGACT
ACACAGCCACTCTGACCCTAGGAGATCCAGACCTGATTGGAGAATTGGTGATCATGGTGGTCACATCCTACAGGTCCTCA
CCTATCGGCTAGGAGTAGGGCAAGAGCTAGTGTACCCCCATTGGCCAAGCAAAAAGGGAGTCATCTTGACACTGGCTCGG
ACGGGCCGGGCTGTACACTGGGAAGCTATATGGACTGTAGTCAGGCAGGAGGGCATGCAGGTTAGTACCACGAGCAAATG
AACAGATTGAGGTTGGAGTGGAATCTGAAGCAAACACAAGGCTACAGGATACAACCTTCTCCTTTGGTTACCACCTCACA
CGGCCC

Alignment

ORF - retro_etel_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.47 %
• Parental protein coverage: 79.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAVPRRTPRRE-EPLPNPGSFDELHRLCKDVFPAQMEGVKLVVNKVLSSHFQVAHSVHMSALGLPGYHLH
          G..P.R.......PLPN.GSF..LH..CK.V..AQ.EGVKL.VNK.LSSHFQV.H.V.M.AL....YHLH
Retrocopy GLCPTRSSAQPWDPLPNSGSFNALHGICKEVSLAQTEGVKLIVNKILSSHFQVVHTVNMKALS---YHLH

Parental  AVYAGDCQLSPSEVFPTVVGDMDSSGSLNAQVLLLLAERLRTKAVFQTQQAKFLTWQFDGEYRGDDYTAT
          A..AGDC.LSPSEVFP.VV..MDSSGSLNA.VLLLLAERLR.K.VFQ..QAKF..WQFD.EYRGDDYTAT
Retrocopy AIHAGDCPLSPSEVFPIVVRNMDSSGSLNARVLLLLAERLRAKVVFQMHQAKFQMWQFDSEYRGDDYTAT

Parental  LTLGNPDLIGESVIMV-AHFLQSLTHRLVLGGELVYHRRPGEEGAILTLAGKYSAVHWEAT-LNVGSGGA
          LTLG.PDLIGE.VIMV..H.LQ.LT.RL..G.ELVY...P...G.ILTLA....AVHWEA........G.
Retrocopy LTLGDPDLIGELVIMV<GHILQVLTYRLGVGQELVYPHWPSKKGVILTLARTGRAVHWEAI<MDCSQAGG

Parental  HASYYH-KANEQVQVGVEFEANTRLQDTTFSFGYHLTLP
          HA..YH..ANEQ..VGVE.EANTRLQDTTFSFGYHLT.P
Retrocopy HAG*YH<RANEQIEVGVESEANTRLQDTTFSFGYHLTRP

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_1124 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000004808	1 retrocopy	retro_eeur_472,
Echinops telfairi	ENSETEG00000015755	2 retrocopies	retro_etel_1124 , retro_etel_1461,
Gorilla gorilla	ENSGGOG00000005720	2 retrocopies	retro_ggor_1075, retro_ggor_1761,
Otolemur garnettii	ENSOGAG00000013733	1 retrocopy	retro_ogar_2524,
Ictidomys tridecemlineatus	ENSSTOG00000003800	2 retrocopies	retro_itri_301, retro_itri_724,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,