RetrogeneDB ID: retro_etel_2052

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_42584:221..1063(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000009460
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB40C
• Ensembl ID: ENSETEG00000005311
• Aliases: None
• Description: RAB40C, member RAS oncogene family [Source:HGNC Symbol;Acc:18285]

Sequence

>retro_etel_2052
ATGGGGACGCAGGGCAGCCCGGTGAAAGAGCTACGACTACCTGCTCAAGTTTCTGCTGGTGGGCGATAGCGACGTGGGCA
AGGGCGAGATCCTGGAGAGCCTGCAGGACGGCGCCTCCGAGTCGCCCTACGCTTACAGCAACGGCATTGACTACAAAACC
ACCACCATCCTGCTGGACGGCCGCCGAGTGAAGCTGGAGCTCTGGGACACCTCAGGCCAGGGCAGGTTCTGCACCATGTT
CAGGTCCTACTCCCGCGGCGCACAGGGCATCCTCCTAGTGTACGACATCACTAACCGCTGGTCCTTTGACGGCATCGACC
GGTGGATCAGGGCGATTGATGAGCACGCACCCGGGGTCCCCCGGATCCTGGTAGGGAACCGGCTGCACCTGGCCTTCAAG
CGGCAGGTGCCCACAGAGCAGGCGCGCGCCTACGCCGAGAAGAACTGCATGACCTTCTTTGAGGTCAGCCCGCTGTGCAA
CTTCAACGTGACGGAGTCCTTCACGGAGCTCTCGCGCATCGTGCTCATGCGCCACGGCATGGAGAAGATCTGGAGGCCCA
ACCGAGTGTTCAGTCTGCAGGACCTGTGCTGCCGTGCCATCGTGTCCTGTACGCCGGTCCACCTCATCGACAAGCTCCCG
CTGCCCGTCACCATTAAGAGCCACCTCAAGTCCTTCTCCATGGCCAACGGCATGAACGCCGTCATGATGCACGGCCGCTC
CTACTCGCTGGCGGGCGGGGGCGGGGGCGGGGGCAGCAAGGGCAGCAGCCTCAAACGCTCCCGCTCTATCCGCCCCTCCC
AGAGCCTCCCCCCAGAACTGCTCCCGCAGCAACTGTAAGATC

Alignment

ORF - retro_etel_2052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.97 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGTQGSPVK-SYDYLLKFLLVGDSDVGKGEILESLQDGASESPYAYSNGIDYKTTTILLDGRRVKLEIWD
          MGTQGSPVK.SYDYLLKFLLVGDSDVGKGEILESLQDGASESPYAYSNGIDYKTTTILLDGRRVKLE.WD
Retrocopy MGTQGSPVK>SYDYLLKFLLVGDSDVGKGEILESLQDGASESPYAYSNGIDYKTTTILLDGRRVKLELWD

Parental  TSGQGRFCTIFRSYSRGAQGILLVYDITNRWSFDGIDRWIREIDEHAPGVPRILVGNRLHLAFKRQVPTE
          TSGQGRFCT.FRSYSRGAQGILLVYDITNRWSFDGIDRWIR.IDEHAPGVPRILVGNRLHLAFKRQVPTE
Retrocopy TSGQGRFCTMFRSYSRGAQGILLVYDITNRWSFDGIDRWIRAIDEHAPGVPRILVGNRLHLAFKRQVPTE

Parental  QARAYAEKNCMTFFEVSPLCNFNVTESFTELSRIVLMRHGMEKIWRPNRVFSLQDLCCRAIVSCTPVHLI
          QARAYAEKNCMTFFEVSPLCNFNVTESFTELSRIVLMRHGMEKIWRPNRVFSLQDLCCRAIVSCTPVHLI
Retrocopy QARAYAEKNCMTFFEVSPLCNFNVTESFTELSRIVLMRHGMEKIWRPNRVFSLQDLCCRAIVSCTPVHLI

Parental  DKLPLPVTIKSHLKSFSMANGMNAVMMHGRSYSLAGGGGGGGSKGSSLKRSRSIR-PPQSPPQNCSRSNC
          DKLPLPVTIKSHLKSFSMANGMNAVMMHGRSYS.........SKGSSLKRSRSIR.PP...PQNCSRSNC
Retrocopy DKLPLPVTIKSHLKSFSMANGMNAVMMHGRSYSXXXXXXXXXSKGSSLKRSRSIR>PPRASPQNCSRSNC

Parental  KI
          KI
Retrocopy KI

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_2052 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000036629	1 retrocopy	retro_cjac_3074,
Echinops telfairi	ENSETEG00000005311	1 retrocopy	retro_etel_2052 ,