RetrogeneDB ID: retro_etel_1802

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_298948:9554..10730(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000018135
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSETEG00000001392
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]

Sequence

>retro_etel_1802
AAAATGCTCGCCGCGGTGATGTCCCGTGTGCTGTCGAGAGTGGCTGCCCAGAAGCCTGCCAACAGGGTGCTGGTGGGCTC
CTGTCACTATTCCAAACAGGCTACGTTTGAAATTAAGAAATGCGATCTCTATCAAATGGACGAGGGCCCTCCTGCCTCCA
CCGAGCTCACCAGGGAGGATGGGCTCAAGTACTACCGGCTGATGCAGACTGTCCGCCGCCTGGAATTAAAGGCCGATCAG
CTGTATAAGCAGAAATTTATCCGTGGGTTCTGTCACTTGTGCGATGGCCAGGAAGCCTGTTGTGTCGGCATCGAGGCAGG
CATAAACCCCACGGATCACGTCATCACATCCTATCGGGCTCATGGCTTATGCCCTTACGCGGGGCATTTCTGCCCGGGCA
ATTCTCGCCGAGCTTACGGGCAGAAGAGGAGGTTGTGCCAAAGGAAAAGGCGGATCGATGCATATGTACGCCAACCACTT
CTATGGGGGCAATGGCATTGTGGGAGCTCAGGTACCCCTGGGAGCCGGCATTGCTTTGGCCTGTAAATATAAAGAAAACA
AAGAAGTCTGTCTGACCCTATATGGGGATGGCGCTGCCAACCAGGGTCAGCTATTTGAAGTTTACAATATGGCCGCTTTG
TGGAAACTACCGTGCATTTTCATCTGCGAAAATAATCGTTATGGAATGGGAACGTCGGTGGAGAGAGCAGCCGCCAGCAC
CGACTATTACAAGCGAGGTCATTTTATTCCGGGGATACGGGTAGACGGGAATGGACATGTCCTGTTGCGTTCCGGGAGGC
AACCAAATTTGCTGCCAACCATTGTAGATCTGGGAAGGGGCCCATACTGATGGAGCTGCAGACCTACCGTTATCACGGAC
ACAGTATGAGTGATCCCGGAGTCAGCTATCGTTCCAGAGAAGAAATTCAGAAAGTCAGAAGTAAGAGCGACCCCATTATG
CTTCTCAAGGACAGGATGGTGAACAACGACCTCGCCAGTGTGGAAGAGCTCAAGGAAATCGACGTGGAAGTGAGAAAGGA
AATCGAGGATGCAGCCCAGTTTGCTACAGCAGATCCGGAACCGCCTCTGGAAGAACTGGGGTATCACATCTACTGCAACG
ACCCGCCTTTTGAAGTTCGTGGTGCAAATCAGTGGATTAAATTCAAGTCAGTCAGT

Alignment

ORF - retro_etel_1802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.53 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KMLAAV-SRVLLG-AAQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPETTVLTREDGLRYYRMMQT
          KMLAAV.SRVL...AAQKPA.RVLV.S......ATFEIKKCDL....EGPP..T.LTREDGL.YYR.MQT
Retrocopy KMLAAVMSRVLSRVAAQKPANRVLVGSCHYSKQATFEIKKCDLYQMDEGPPASTELTREDGLKYYRLMQT

Parental  VRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHG-FTFTRGLTVREILAELT
          VRR.ELKADQLYKQK.IRGFCHLCDGQEACCVG.EAGINPTDH.IT.YRAHG....TRG...R.ILAELT
Retrocopy VRRLELKADQLYKQKFIRGFCHLCDGQEACCVGIEAGINPTDHVITSYRAHG>YALTRGISARAILAELT

Parental  GRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYN
          GRRGGCAKGKGGSMHMYA..FYGGNGIVGAQVPLGAGIALACKY....EVCLTLYGDGAANQGQ.FE.YN
Retrocopy GRRGGCAKGKGGSMHMYANHFYGGNGIVGAQVPLGAGIALACKYKENKEVCLTLYGDGAANQGQLFEVYN

Parental  MAALWKLPCI-ICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDG-MDI-LCV-REATKFAAAHCRAG
          MAALWKLPCI.ICENNRYGMGTSVERAAASTDYYKRG.FIPG.RVDG.MD...CV.REATKFAA.HCR.G
Retrocopy MAALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGHFIPGIRVDG>MDMSCCV>REATKFAANHCRSG

Parental  KGPILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNNDLASVEELKEIDVEVRKEI
          KGPILMELQTYRYHGHSMSDPGVSYR.REEIQ.VRSKSDPIMLLKDRMVNNDLASVEELKEIDVEVRKEI
Retrocopy KGPILMELQTYRYHGHSMSDPGVSYRSREEIQKVRSKSDPIMLLKDRMVNNDLASVEELKEIDVEVRKEI

Parental  EDAAQFATADPEPPLEELGYHIYSSDPPFEVRGANQWIKFKSIS
          EDAAQFATADPEPPLEELGYHIY..DPPFEVRGANQWIKFKS.S
Retrocopy EDAAQFATADPEPPLEELGYHIYCNDPPFEVRGANQWIKFKSVS

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_1802 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
Echinops telfairi	ENSETEG00000001392	1 retrocopy	retro_etel_1802 ,
Loxodonta africana	ENSLAFG00000009426	1 retrocopy	retro_lafr_91,
Macaca mulatta	ENSMMUG00000017336	1 retrocopy	retro_mmul_123,
Procavia capensis	ENSPCAG00000004196	1 retrocopy	retro_pcap_451,
Sarcophilus harrisii	ENSSHAG00000015375	1 retrocopy	retro_shar_84,