RetrogeneDB ID: retro_etel_1455

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_268977:3257..3843(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSBP3
• Ensembl ID: ENSETEG00000000453
• Aliases: None
• Description: single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674]

Sequence

>retro_etel_1455
CCCAGTGGAATGGACCCAACTCGACAACAAGGACACCCAAATATGGGTGGGCCAATGCAGAGAATGACTACTCCAAGAGG
AATGGTGCCTTTAGGACCACAGAATTATGCAGGTGCAATGAGACCCCACTGAATGCTTTAGGTGGCCCTGGAATACCTGG
AATGAGTCCAGGTGGTGGCAGACCTTGGCCAAATCCAACAAATGCCAATTCAATACCATACTCCTCAGCATCTCCTGGGA
ATTGTGTAGGTCCTCCAGGAGGTGGAGGGCCACCAGGAACACCCATCATGCCTAGTCCTGAAGATTCAACCAACTCTGGA
GACAATATGTACACTTTAATGAATGCAGTACCTCCTGGACCTAACAGACCTAATTTTCCAATGGGCCCTGGGTCAGATGG
TCCAATGGTTGGATTAGGAGGAATGGAGTCACATCACATGAATGGCTCTTTACGCTCAGGAGATATGGACAGTATTTCCA
AGAATTTTCCCAATAACATGAGCCTGAATAATCAGCCGGGCACTCCAAGGGATGATGGCGAGATGAGGGGGAATTTCTTA
AATCCTTTCAGAGTGAGAGTTACTCC

Alignment

ORF - retro_etel_1455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.07 %
• Parental protein coverage: 61.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PNSMDPTRQQGHPNMGGSMQRMNPPRGMGPMGPGPQNYGSGMRP-PPNSLG-PAMPGINMGPGAGRPWPN
          P..MDPTRQQGHPNMGG.MQRM..PRGM.P.GP..QNY...MRP.P.N.LG.P..PG..M.PG.GRPWPN
Retrocopy PSGMDPTRQQGHPNMGGPMQRMTTPRGMVPLGP--QNYAGAMRP<PLNALGGPGIPG--MSPGGGRPWPN

Parental  PNSANSIPYSSSSPGTYVXXXXXXXXXXXXXXXXXXXSTNSSDNIYTMINPVPPGGSRSNFPMGPGSDGP
          P..ANSIPYSS.SPG..V...................STNS.DN.YT..N.VPPG..R.NFPMGPGSDGP
Retrocopy PTNANSIPYSSASPGNCVGPPGGGGPPGTPIMPSPEDSTNSGDNMYTLMNAVPPGPNRPNFPMGPGSDGP

Parental  MGGMGGMEPPHMNRSLGSGDIDGLPKNSPNNISGISNPPGTPRDDGELGGNFLH-SFQNDNYS
          M.G.GGME..HMN.SL.SGD.D...KN.PNN.S...N.PGTPRDDGE..GNFL..SFQ...YS
Retrocopy MVGLGGMESHHMNGSLRSGDMDSISKNFPNNMS-LNNQPGTPRDDGEMRGNFLN<SFQSESYS

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_1455 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019045	1 retrocopy	retro_cfam_1684,
Echinops telfairi	ENSETEG00000000453	1 retrocopy	retro_etel_1455 ,