RetrogeneDB ID: retro_etel_1041

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_203334:6938..8111(-)
• 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_1041
GAAGCCGACAACGCAGAGATGAGGGCCTCACGGATCCTGCACGGGCTGGGCTTCACCCCCGCCGTGCAGCGCAAGCAGCT
CAAGGACTTCAGTGGAGGCTGGAGGATGAGGGTTGCCCTCGCCAGAGCCCTCTTTATTCGGCCCTTCATGCTGCTCCTGG
ACGAGCCCTCCAACCACTTGGCCCTCGATGCCTGTGTGTGGTCAGAAGAAGAACTCAAGGCTTCTAAGCATATCCTGGTC
CTCGTCTCTCAGTCCCAAGATTTCCTGAATGGTGTGTGCACCAGCATCGTTCACATGCACAACAAGAAACTGCAGTATTA
TACGGGTAATTATGACCAGTACGCGAAGACTCGGCTGGACCTAGAGGAGAACCAGACGAAGCACGTCCCATGGGAACAGG
ACCAGATGGCACGCATGAAGAACTAGATCGCCAGGTTTGGCCATGGCAGTGCCAAGTTGGCCCGGCAGGCCCAGAGCAAA
GAGAAGACGCTACAGAAAATGATGGCATCGGGCCTGACAGAACGGGTTGTTAGTGACAAGACACTATCGTTTTATTTCCC
ACCATGTGGCAAGATCCCTCCACCAGTCATTATGGTACAAAACGTGAGCTTCAGGTATACGAAAGATGGGCCTTGCATCT
ACAACAACCTAGAGTTTGGCATTGACCTCGACACACGAGTGGCTCTGTAGGGCCCAGTGGAGCAGGGAAGTCAACGCTTT
CGAAGCTGTTAACTGGAGAGCTACTCCCCACAGACGGCATGATCCAAAAACATTCTCATGTCAAGATAGGGCGTTACCAT
CGGCATTTACAGGAGCAGCTGGATTTGGATCTCTCTCCTTTGGAGTACATGATGAAATGCTACCGGAAATCAAGGAGAAG
GAAGAAATGAGGAAGATCATTGGACGATATGGTCTCCCTGGGAAAAGCAGGTGAGCCCAATCCAGAACCTATCCGATGGC
CAGAAGTGCCGTGTGTGCCTGGCCTGGCTGGCCTGGCAGAACCCGCACCTGCTCTTCCTGGACGAGCCTACCAATCACCT
GGACATTGAGACCATCGATGCGCTGGCTGATGCCATCAATGAGTTTGAAGGTGGCATGATGCTGGTCAGCCATGACTTCA
GACTCATCCAGCAGGTGGCACAAGAAATCTGGGTCTGTGACAATCACCAAGTG

Alignment

ORF - retro_etel_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.38 %
• Parental protein coverage: 61.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DADKAEMRASRILHGLGFTPAMQRKKLKDFSGGWRMRVALARALFIRPFMLLLDEPTNHLDLDACVWLEE
          .AD.AEMRASRILHGLGFTPA.QRK.LKDFSGGWRMRVALARALFIRPFMLLLDEP.NHL.LDACVW.EE
Retrocopy EADNAEMRASRILHGLGFTPAVQRKQLKDFSGGWRMRVALARALFIRPFMLLLDEPSNHLALDACVWSEE

Parental  ELKTFKRILVLVSHSQDFLNGVCTNIIHMHNKKLKYYTGNYDQYVKTRLELEENQMKRFHWEQDQIAHMK
          ELK..K.ILVLVS.SQDFLNGVCT.I.HMHNKKL.YYTGNYDQY.KTRL.LEENQ.K...WEQDQ.A.MK
Retrocopy ELKASKHILVLVSQSQDFLNGVCTSIVHMHNKKLQYYTGNYDQYAKTRLDLEENQTKHVPWEQDQMARMK

Parental  NYIARFGHGSAKLARQAQSKEKTLQKMMASGLTERVVSDKTLSFYFPPCGKIPPPVIMVQNVSFRYTKDG
          N.IARFGHGSAKLARQAQSKEKTLQKMMASGLTERVVSDKTLSFYFPPCGKIPPPVIMVQNVSFRYTKDG
Retrocopy N*IARFGHGSAKLARQAQSKEKTLQKMMASGLTERVVSDKTLSFYFPPCGKIPPPVIMVQNVSFRYTKDG

Parental  PCIYNNLEFGIDLDTRVAL-VGPNGAGKSTLLKLLTGELLPTDGMIRKHSHVKIGRYHQHLQEQLDLDLS
          PCIYNNLEFGIDLDTRVAL.VGP.GAGKSTL.KLLTGELLPTDGMI.KHSHVKIGRYH.HLQEQLDLDLS
Retrocopy PCIYNNLEFGIDLDTRVAL<VGPSGAGKSTLSKLLTGELLPTDGMIQKHSHVKIGRYHRHLQEQLDLDLS

Parental  PLEYMMKCY-PEIKEKEEMRKIIGRYGLTGK-QQVSPIRNLSDGQKCRVCLAWLAWQNPHLLFLDEPTNH
          PLEYMMKCY.PEIKEKEEMRKIIGRYGL.GK..QVSPI.NLSDGQKCRVCLAWLAWQNPHLLFLDEPTNH
Retrocopy PLEYMMKCY<PEIKEKEEMRKIIGRYGLPGK<KQVSPIQNLSDGQKCRVCLAWLAWQNPHLLFLDEPTNH

Parental  LDIETIDALADAINEFEGGMMLVSHDFRLIQQVAQEIWVCEKQTI
          LDIETIDALADAINEFEGGMMLVSHDFRLIQQVAQEIWVC.....
Retrocopy LDIETIDALADAINEFEGGMMLVSHDFRLIQQVAQEIWVCDNHQV

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_1041 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,