RetrogeneDB ID: retro_tbel_3670

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148144:99435..99842(-)
• Located in intron of: ENSTBEG00000000202

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELAVL1
• Ensembl ID: ENSTBEG00000015038
• Aliases: None
• Description: ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R) [Source:HGNC Symbol;Acc:3312]

Sequence

>retro_tbel_3670
CACAGCTTGAGCTATGGCTTTGTGAATCACATGACTGTGAAGGACACAATGTACTCAATGCTGAATGGCCTGAGGCTCCA
GTCAAAGACCATTAAGATGCACGTGTGCACGAGCTCCAAGGTTATCAAAGATGAGAACTTGTACATCAGGGGGCTCTGGA
AGACCATGACCCAGAAGGATACGGAAGGTGTGTTCTCTGAGTAGGAATGAATCAACTCATGGGTCCTGGTGATCAGACCA
CAGGTTTGTCCAGAGGGGCTGCGTTTATCTAGCTTGACCAACAGTGGGAAGCAGAAGAGGCCAATCTCAATGGTCATAAA
CTCCCAGGTTCCTCTAAGCCCATTACAATGACGTTCACGGTCAATCTTAACCAGAACAAAAACATGGCACTTCTCTCCCA
ACACTAC

Alignment

ORF - retro_tbel_3670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.68 %
• Parental protein coverage: 52.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSLGYGFVNYVTAKDAERAVNTLNGLRLQSKTIKVWARESTEAFKDATLYISGLPRTMTQKDVEDMFSRF
          HSL.YGFVN..T.KD.......LNGLRLQSKTIK.....S....KD..LYI.GL..TMTQKD.E..FS..
Retrocopy HSLSYGFVNHMTVKDTMYSM--LNGLRLQSKTIKMHVCTSSKVIKDENLYIRGLWKTMTQKDTEGVFSE*

Parental  GRIINSRVLV-DQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFAANPNQNKNMALLSQ
          ..I.NS.VLV.DQTTGLSRG.AFI..D...EAEEA....NGHK.PGSS.PIT..F..N.NQNKNMALLSQ
Retrocopy E*I-NSWVLV<DQTTGLSRGAAFI*LDQQWEAEEA--NLNGHKLPGSSKPITMTFTVNLNQNKNMALLSQ

Parental  LY
          .Y
Retrocopy HY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3670 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3670 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018353	1 retrocopy	retro_cfam_1972,
Choloepus hoffmanni	ENSCHOG00000006810	2 retrocopies	retro_chof_2564, retro_chof_44,
Tupaia belangeri	ENSTBEG00000006133	1 retrocopy	retro_tbel_4280,
Tupaia belangeri	ENSTBEG00000015038	1 retrocopy	retro_tbel_3670 ,