RetrogeneDB ID: retro_etel_947

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_189615:85..491(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000008127
• 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_947
ATGCAGCACTCAGCCTTTCTCCTCCTTGCCCTCGTGGTGCTCACATCCACGGTGGCCAAAAAGAAAGGCAAGGTGAAGAA
GGGTGGCCTGGGTGGCCTGGGCAGTGAATGTGCTGAGTGGGCCTGAGAGCCCTGTATACATTAAGGACACTGGCATGAGT
TTACACAAGGGCATCTGGGGGACCCAGACTCAGTGCATCCCATGTGGAGTGCCCTTCAACTGGAAGAAGGAGTTTGGCGC
CAATTTCAAGTACAAGTTTGAGAGTTGGGATGTTTGTGATTGCACAGTCACCAAGGCCAGCCAAAGCACCCTGAAGAAAG
CTTGGTATAAAGCCCAGTACTAGGAGTCCATCCTCATGATGAAGCGTTCCACAACTAAGACCAAAGCCAAGAAAGGGAAG
AGAAAG

Alignment

ORF - retro_etel_947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.27 %
• Parental protein coverage: 96.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQHRAFLLLALLALTLTSTATKKKDKAKKGGPGGQCAEWAW-GPCTPSS-KDCGVGFREGTCGTQTQRIR
          MQH.AFLLLAL..LT..ST..KKK.K.KKGG.GG...E.A..GP..P...KD.G.....G..GTQTQ.I.
Retrocopy MQHSAFLLLALVVLT--STVAKKKGKVKKGGLGGLGSECAE>GPESPVYIKDTGMSLHKGIWGTQTQCIP

Parental  CRVPCNWKKEFRADCKYKFENWGACDGGTGTKARQGTLKKARYNAQCQDTILVMKPCTPKTKAKAKAKK
          C.VP.NWKKEF.A..KYKFE.W..CD..T.TKA.Q.TLKKA.Y.AQ....IL.MK..T.KTKAK....K
Retrocopy CGVPFNWKKEFGANFKYKFESWDVCD-CTVTKASQSTLKKAWYKAQY*ESILMMKRSTTKTKAKKGKRK

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_947 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,