RetrogeneDB ID: retro_etel_2124

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_68532:2523..3212(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000003450
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP2M1
• Ensembl ID: ENSETEG00000004759
• Aliases: None
• Description: adaptor-related protein complex 2, mu 1 subunit [Source:HGNC Symbol;Acc:564]

Sequence

>retro_etel_2124
ATGATCGGAGGGCTGTTCATCTACAATCACAAAGGGGAGTTGCTCATCTCCTGGGTCTACCTCGATGACATCGGGAGGAA
TGTAGTGGATGCCTTCCGGGTCAATGTTATCCACGCCTGGCAGCAGGTGCGCAGGCCCGTCACCCACATTGCACGGACCA
ACTCCTTCCATGTTAAGCGGTCCAACATCTGGCTGGCAGCTGTCACCAAGCAGAATGTCAATGCTGCCATGGTCTTCGAA
TTCCTCTATAAGATGTGTGACGTGACGGCGGCCTACTTTGGCAAGATCAGCAAAGAGAACATCAAGAACAGCTTTGTGCT
CATCTACGAGTTGCTGGATGAGATCCTGGACTTTGGCTATCCACAGAACTCAGAAACGGGCGCGCGGAAAACCATCATTC
AGCAGGGCATCAAGAGCCAGCATCAGACTTAAGAAGAGCAGTCCCAGATCACCAGCCAGATCGGCTGGCACCAGGAGGGC
TTCAAGTACCGCGCAATGGGCTCTTCCTGGATGTGCTAGAGAGCGTGAACCTGCTCATGTCCCCGCAGGGACAGGTGCTG
AGCGCCCACGTGTTGGGCCGGGTGGTGATGAAGAGCTACCTGAGTGGCATGCCCGAGTGCAAGTTTGGGATGAATGACAA
GATTGTCATCGAGAAGCAGGGCAAGGGCACGGCGGACGAAACAAGCAAG

Alignment

ORF - retro_etel_2124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.14 %
• Parental protein coverage: 54.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTK
          MIGGLFIYNHKGE.LIS.VY.DDIGRN.VDAFRVNVIHA.QQVR.PVT.IART..FHVKRSNIWLAAVTK
Retrocopy MIGGLFIYNHKGELLISWVYLDDIGRNVVDAFRVNVIHAWQQVRRPVTHIARTNSFHVKRSNIWLAAVTK

Parental  QNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKS
          QNVNAAMVFEFLYKMCDV.AAYFGKIS.ENIKN.FVLIYELLDEILDFGYPQNSETGA.KT.I.QQGIKS
Retrocopy QNVNAAMVFEFLYKMCDVTAAYFGKISKENIKNSFVLIYELLDEILDFGYPQNSETGARKTII-QQGIKS

Parental  QHQTKEEQSQITSQVTGQIGWRREGIKYR-RNELFLDVLESVNLLMSPQGEVLSAHVSGRVVMKSYLSGM
          QHQT.EEQSQITSQ.....GW..EG.KYR.RN.LFLDVLESVNLLMSPQG.VLSAHV.GRVVMKSYLSGM
Retrocopy QHQT*EEQSQITSQI----GWHQEGFKYR<RNGLFLDVLESVNLLMSPQGQVLSAHVLGRVVMKSYLSGM

Parental  PECKFGMNDKIVIEKQGKGTADETSK
          PECKFGMNDKIVIEKQGKGTADETSK
Retrocopy PECKFGMNDKIVIEKQGKGTADETSK

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_2124 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012998	1 retrocopy	retro_cjac_3340,
Erinaceus europaeus	ENSEEUG00000006073	1 retrocopy	retro_eeur_47,
Echinops telfairi	ENSETEG00000004759	1 retrocopy	retro_etel_2124 ,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98,
Tarsius syrichta	ENSTSYG00000006101	1 retrocopy	retro_tsyr_1873,