RetrogeneDB ID: retro_etel_1908

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_312883:170621..171194(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRNP48
• Ensembl ID: ENSETEG00000011102
• Aliases: None
• Description: small nuclear ribonucleoprotein 48kDa (U11/U12) [Source:HGNC Symbol;Acc:21368]

Sequence

>retro_etel_1908
CTTTATTCTTCACTGTCTTTTGAAGTACCTCTGAAGCATAAATGGTGCTTTTGTTGTCTAATTCAAGCTGATCGCCAAAA
ATCTTTGATTTTGTAGTTGAAGAAACAAAAAAGGAGAAGCACTCAAATGCTCAAATCACTGAAAATGACAGCGATCTTTT
TGCAGCCTTGGCAGCTAAAGTCAATCAAGTAAATAGCTGAAAATGTCCAAAATCATACCTTGACATTCTGGCAGAAGTGA
TTGATTGTAAAAGAAGATGCCAGTCCTAAGAGTTAAGAATGCTCACATAACCAAGAGGTCATACACTGCGCTGGTCCGGG
ATGCGATACATGTGCACATGGAAGAACTCTGCAATCAGGGGCAAGATGAGCAGGATGAAGTAGATTACAGTGCTCTACAG
GAGGGAGACAGGGGATCAGCTTCTGTAGATTCATGGCAGTCTGGGGGAAGCTATTTGGATGCCGAGTGTTCACAGCAGAG
AAGGGATCAGCGTAGGAGCCAGCACAAATGAAAGAAAGTAAAGATAGGGATAGAAACAACCTCAGAAGAAGGAAATAGAG
GGAAGAGAAATAT

Alignment

ORF - retro_etel_1908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.26 %
• Parental protein coverage: 56.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IYSSVPVEVPLNHKRFVCDLTQADRRA-IYDFVVEETKK-KQSSSQITENDSDLFVDLAAKVNQDNSRKC
          .YSS...EVPL.HK...C.L.QADR...I.DFVVEETKK.K.S..QITENDSDLF..LAAKVNQ.NS.KC
Retrocopy LYSSLSFEVPLKHKWCFCCLIQADRQK<IFDFVVEETKKEKHSNAQITENDSDLFAALAAKVNQVNS*KC

Parental  PKSYLEILAEVRDYKRRRQS-YRAKNVHITKKSYTEVIRDVINVHMEELSNQWQDEQEKAEDGAMKEGDR
          PKSYL.ILAEV.D.KRR.QS..R.KN.HITK.SYT...RD.I.VHMEEL.NQ.QDEQ......A..EGDR
Retrocopy PKSYLDILAEVIDCKRRCQS<LRVKNAHITKRSYTALVRDAIHVHMEELCNQGQDEQDEVDYSALQEGDR

Parental  GSASVDSWQSGGSYLDAECSQQRRDQRRSQHKKSK-ERDR--NNLRRRKRDGERH
          GSASVDSWQSGGSYLDAECSQQRRDQRRSQHK..K...DR..NNLRRRK...E..
Retrocopy GSASVDSWQSGGSYLDAECSQQRRDQRRSQHK*KK<SKDRDRNNLRRRK*REEKY

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_1908 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011102	1 retrocopy	retro_etel_1908 ,