RetrogeneDB ID: retro_etel_1929

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_315959:43638..44046(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000003085
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MDK
• Ensembl ID: ENSETEG00000016707
• Aliases: None
• Description: midkine (neurite growth-promoting factor 2) [Source:HGNC Symbol;Acc:6972]

Sequence

>retro_etel_1929
ATGCAACACAGAGCCTTCCTCCTTCTTGCCCTCCTGACCCTACTGGCTCTCCTTTCCATGGTAGCTAAAAAGAAAGACAA
AGTGAAGAAGGGAAGTTTTGGCAGCAAGTGCCTGGTGTGGGCTTAGAGCCTTGTGCCCCAGCAGCAAAGACTGTGGAGTG
TGTTTCTGAGAGGGCACCTGTGTGACCCAGAACCAGCGCTTCCCATGCATGGTCCCCAGCAACTAGTTTGGAGCCATCTG
CAAGTACAAATTTGAGAGCCAAGATGTGTGTGATGGGGTACAAACATCAAAGCCCACCAAGGCACCCTGAACAAGGTGCG
GTAGAATGCCCAGTGTGAGAATACTATCTCCATGATGAAGCCTTGCATCCCTAAGATGAAAGCCAAGACCAAAGCCAAGA
AAGGGAAG

Alignment

ORF - retro_etel_1929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 97.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQHRAFLLLALLAL-TLTSTATKKKDKAKKGGPGGQCAEWAWG-PCTP-SSKDCGVGFREGTCGTQTQRI
          MQHRAFLLLALL.L..L.S...KKKDK.KKG..G..C..WA...PC.P.SSKDCGV.F.EGTC.TQ.Q..
Retrocopy MQHRAFLLLALLTLLALLSMVAKKKDKVKKGSFGSKCLVWA*S<PCAP<SSKDCGVCF*EGTCVTQNQ--

Parental  RCRVPCNWKKE-FRADCKYKFENWGACDG-GTGTKARQGTLKKARYNAQCQDTILVMKPCTPKTKAKAKA
          ..R.PC......F.A.CKYKFE....CDG.GT..KA.QGTL.K.R.NAQC..TI..MKPC.PK.KAK.KA
Retrocopy --RFPCMVPSN*FGAICKYKFESQDVCDG<GTNIKAHQGTLNKVR*NAQCENTISMMKPCIPKMKAKTKA

Parental  KKGK
          KKGK
Retrocopy KKGK

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_1929 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007740	1 retrocopy	retro_btau_655,
Echinops telfairi	ENSETEG00000016707	2 retrocopies	retro_etel_1929 , retro_etel_947,
Loxodonta africana	ENSLAFG00000015119	1 retrocopy	retro_lafr_194,
Macaca mulatta	ENSMMUG00000021448	2 retrocopies	retro_mmul_1486, retro_mmul_466,