RetrogeneDB ID: retro_etel_1058

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_205165:2504..3497(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ABCF2
• Ensembl ID: ENSETEG00000008032
• Aliases: None
• Description: ATP-binding cassette, sub-family F (GCN20), member 2 [Source:HGNC Symbol;Acc:71]

Sequence

>retro_etel_1058
GAAGCCGACAAGGCAGAGATGAGGGCCTCACGGATCCTGCACGGGCTGGGCTTCACCCCCGCCTTGCAGCGCAAGCAGCT
CAAGGACTTCAGTGGAGGCTGGAGGATGAGGGTTGCCCTCGCCAGAGCCCTCTTTATTCGGCCCTTCATGCTGCTCCTGG
ACGAGCCCTCCAACCACTTGGACCTTGATGCCTTTGTGCGGTTAGAAGAACTCAAGACTTTTACGCGTATCCTGGACCTC
GTCTCTCATTCCCGAGATTTCCTGAATGGTGTGTGCACCAGCATCGTTCACATGCACAAGAAACTGCAGTATTATACGGG
TAATTACGACCAGTACGCGAAGACTCGACTGGAGCTAGAGGAGAACCAGACGAAGCGCGTCCACTGGGAACAGGACCAGA
TCACGCACATGAAAAACTAGGTCGCCAGGTTTGCCATGGCAGTGCCAAGTTGGCCCGGCAGGCCCAGAGCAAAGAGAAGA
CACTACAGACAATGATGGCATTGGGCCTGGCAGAGCGGGTTGTTCGTGACAAGACACTATTGTTTTATTTCCCACCATGT
GGCAAGATCCCTCCACCAGTCATTATGGTACAAAACGTGAGCTTCAGGTATACGAAAGATGGGCCTTGCATCTACAACAA
CCTAGAGTTTGGCATTGTCCTCCACAGATGAGTGGCTCTGGTAGGGCCCAGTGGAGCAGGGAAGTCAACGCTTTTGAAGC
TGTTAACTGGAGAGCTACTCCCCACAGACGGCATGATCCGAAAACACTCTCATGTCAAGATAGGGCGTTACCATCGGCAT
TTACAAGAGCAGCTGGATTTGGATCGCTCTCCTTTGGAGCACATGAGGAAGTGCCACCCGGAAATCAAGGAGAAGGAAGA
AATGAGGAAGATCATTGGACGATATGGTCTCCCTGGGAAACAGCAGGTAAGCCCAATCCGGAACCTATCTGATGGCCAGA
AGTGCCGTGTGTGCCTGGGCCTGGCTGGCCTGG

Alignment

ORF - retro_etel_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.36 %
• Parental protein coverage: 52.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DADKAEMRASRILHGLGFTPAMQRKKLKDFSGGWRMRVALARALFIRPFMLLLDEPTNHLDLDACVWLEE
          .ADKAEMRASRILHGLGFTPA.QRK.LKDFSGGWRMRVALARALFIRPFMLLLDEP.NHLDLDA.V.LEE
Retrocopy EADKAEMRASRILHGLGFTPALQRKQLKDFSGGWRMRVALARALFIRPFMLLLDEPSNHLDLDAFVRLEE

Parental  ELKTFKRILVLVSHSQDFLNGVCTNIIHMHNKKLKYYTGNYDQYVKTRLELEENQMKRFHWEQDQIAHMK
          .LKTF.RIL.LVSHS.DFLNGVCT.I.HMH.KKL.YYTGNYDQY.KTRLELEENQ.KR.HWEQDQI.HMK
Retrocopy -LKTFTRILDLVSHSRDFLNGVCTSIVHMH-KKLQYYTGNYDQYAKTRLELEENQTKRVHWEQDQITHMK

Parental  NYIARFG-HGSAKLARQAQSKEKTLQKMMASGLTERVVSDKTLSFYFPPCGKIPPPVIMVQNVSFRYTKD
          N..ARF..HGSAKLARQAQSKEKTLQ.MMA.GL.ERVV.DKTL.FYFPPCGKIPPPVIMVQNVSFRYTKD
Retrocopy N*VARFA<HGSAKLARQAQSKEKTLQTMMALGLAERVVRDKTLLFYFPPCGKIPPPVIMVQNVSFRYTKD

Parental  GPCIYNNLEFGIDLDTRVALVGPNGAGKSTLLKLLTGELLPTDGMIRKHSHVKIGRYHQHLQEQLDLDLS
          GPCIYNNLEFGI.L...VALVGP.GAGKSTLLKLLTGELLPTDGMIRKHSHVKIGRYH.HLQEQLDLD.S
Retrocopy GPCIYNNLEFGIVLHR*VALVGPSGAGKSTLLKLLTGELLPTDGMIRKHSHVKIGRYHRHLQEQLDLDRS

Parental  PLEYMMKCYPEIKEKEEMRKIIGRYGLTGKQQVSPIRNLSDGQKCRVCL-AWLAW
          PLE.M.KC.PEIKEKEEMRKIIGRYGL.GKQQVSPIRNLSDGQKCRVCL.AWLAW
Retrocopy PLEHMRKCHPEIKEKEEMRKIIGRYGLPGKQQVSPIRNLSDGQKCRVCL>AWLAW

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_1058 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004830	1 retrocopy	retro_cfam_1612,
Callithrix jacchus	ENSCJAG00000020371	3 retrocopies	retro_cjac_1859, retro_cjac_3526, retro_cjac_381,
Dipodomys ordii	ENSDORG00000012672	1 retrocopy	retro_dord_334,
Echinops telfairi	ENSETEG00000008032	2 retrocopies	retro_etel_1041, retro_etel_1058 ,
Macaca mulatta	ENSMMUG00000006679	1 retrocopy	retro_mmul_1414,
Oryctolagus cuniculus	ENSOCUG00000000245	1 retrocopy	retro_ocun_765,