RetrogeneDB ID: retro_etel_1980

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_321510:639..1176(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000009393
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSETEG00000004125
• Aliases: None
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_etel_1980
AACGACAAGCAGGAAGATGTGTTTGTGCAGCAGACGGCCATAAAGAACAGCCCCGGGAAGTCCCTTCTCAGCGCAGGGGA
TGGCGCGACTGTGGGGGTTGTGCTGGAGGAGAAAAGGGCGCCCAGACAGCAGATGTTACAGGTCCCGGTGGCGTCCCCAT
GCCAGGCAGTCACTAGACAGCCGACTGTAACCATTGTAGGCCTTGCCCATGTTGTAGGGGGCCTCCACGCAACTTCCAGC
ACAATTCCCAGAAAAGCGAGAGTTGGGAAAAGGAGGAGGGATGGGAGAATGCTGCTGAAGACCAGGCCCCACAGCACCGG
CCCCTACCGCAGGCGACGGGCCCCACCTCGCTACATGCTGAGACCCTACGGGTGTCGACCATGGTGTTCCAACCCTCCCG
TGGCAGGAGAAGTGATGGAGGGTGCTGACCACTTGGGTGCAGGAGAACAAGGTAGACCAGTGAGACAGAGAATGTACTGA
GGCTATAGACCATAGTTTCACAGGGGCCCTCCTTGCTGCCCCCGCCGGCGCCCAGAT

Alignment

ORF - retro_etel_1980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.03 %
• Parental protein coverage: 56.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK-GAEAANVTGPGGVPVQGSKYAADRNHYR
          ND..EDVFV.QTAI.KN.P.K.L.S.GDG.TV...V.E....GA..A.VTGPGGVP..GS...AD.NH.R
Retrocopy NDKQEDVFVQQTAI-KNSPGKSLLSAGDGATVGV-VLEEKR<GAQTADVTGPGGVPMPGSH*TADCNHCR

Parental  RYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRR-PYRRRRFPPYYMRRPYGRRPQYSNPPVQG
          ..P..RGPPRN.Q.N.Q.SES.EK.EG.E.A.E.QA.Q.R.PYRRRR.PP.YM.RPYG.RP..SNPPV.G
Retrocopy PCPCCRGPPRNFQHNSQKSESWEKEEGWENAAEDQAPQHR>PYRRRRAPPRYMLRPYGCRPWCSNPPVAG

Parental  EVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPRED
          EVMEGAD..GAGEQGRPVRQ.MY.GYRP.F.RGPP.....R.D
Retrocopy EVMEGADHLGAGEQGRPVRQRMY*GYRP*FHRGPPCCPRRRPD

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_1980 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 13 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016627	1 retrocopy	retro_dord_625,
Echinops telfairi	ENSETEG00000002557	1 retrocopy	retro_etel_1898,
Echinops telfairi	ENSETEG00000004125	3 retrocopies	retro_etel_1772, retro_etel_1980 , retro_etel_2134,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Mustela putorius furo	ENSMPUG00000013922	6 retrocopies	retro_mputfur_1154, retro_mputfur_1332, retro_mputfur_1436, retro_mputfur_1627, retro_mputfur_215, retro_mputfur_293,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Ochotona princeps	ENSOPRG00000008050	11 retrocopies	retro_opri_1097, retro_opri_1114, retro_opri_115, retro_opri_1196, retro_opri_340, retro_opri_367, retro_opri_626, retro_opri_781, retro_opri_896, retro_opri_910, retro_opri_984,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,
Sus scrofa	ENSSSCG00000028485	3 retrocopies	retro_sscr_1157, retro_sscr_255, retro_sscr_256,
Ictidomys tridecemlineatus	ENSSTOG00000000116	1 retrocopy	retro_itri_1532,
Tupaia belangeri	ENSTBEG00000015642	9 retrocopies	retro_tbel_1183, retro_tbel_1955, retro_tbel_2347, retro_tbel_2694, retro_tbel_2702, retro_tbel_2961, retro_tbel_3590, retro_tbel_4037, retro_tbel_4478,