RetrogeneDB ID: retro_etel_1594

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_281609:4660..5107(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS1
• Ensembl ID: ENSETEG00000002718
• Aliases: None
• Description: GINS complex subunit 1 (Psf1 homolog) [Source:HGNC Symbol;Acc:28980]

Sequence

>retro_etel_1594
GATAGACTCAGAGAAATTCTGGAGGAGATGAAGGCTTTCTATGAACAAAACCAATCCGATGTTAATGAAGCAAAATCAGA
TGGAAGAAGCAATTTGATACCAACCATCAAATTTCGGCACCGTTCTTTGTTAAGAAATCGACGCTGCACTACTACATGCT
TATGTGGCCGGTTACTTCAGATTAGAGCACTTAGGTGGGAACATGGCAGTGTGTTGCCTAATGCTTTATGGTTTCACACG
TCTGCTGAAGCAATGGAATGGTTCAATTGTTCTAAGAAGTCCCTTGCTGCTTATGTGAGGTCATTGGGAGGAAATAAGGG
TTTGGACATTACACAGGATATGAAGCCACCCAAAAGATTATATATTGAAGTACAGTGTCTAAAAGACTATGGAGAATTTG
AAGTTGATGATGGTACCTCTGTGATACTAAGAACAAGCAGCCAGCAT

Alignment

ORF - retro_etel_1594 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.55 %
• Parental protein coverage: 76.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGLRQILEEMKVLYEQNQSNVNEAKSDGRSNLIPTIKFRHCSLLRNRRCTIAYLYDRLLRIRALRWEYGS
          D.LR.ILEEMK..YEQNQS.VNEAKSDGRSNLIPTIKFRH.SLLRNRRCT...L..RLL.IRALRWE.GS
Retrocopy DRLREILEEMKAFYEQNQSDVNEAKSDGRSNLIPTIKFRHRSLLRNRRCTTTCLCGRLLQIRALRWEHGS

Parental  VLPNALRFHMSAEEMEWFNCYKKSLTTYMRSLGGNEGLDITQDMKPPKSLYIEVRCLRDYGEFEVDDGTS
          VLPNAL.FH.SAE.MEWFNC.KKSL..Y.RSLGGN.GLDITQDMKPPK.LYIEV.CL.DYGEFEVDDGTS
Retrocopy VLPNALWFHTSAEAMEWFNCSKKSLAAYVRSLGGNKGLDITQDMKPPKRLYIEVQCLKDYGEFEVDDGTS

Parental  VILRKNSQH
          VILR..SQH
Retrocopy VILRTSSQH

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_1594 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002718	1 retrocopy	retro_etel_1594 ,
Macropus eugenii	ENSMEUG00000016481	1 retrocopy	retro_meug_1309,
Monodelphis domestica	ENSMODG00000006443	1 retrocopy	retro_mdom_1191,
Rattus norvegicus	ENSRNOG00000008091	1 retrocopy	retro_rnor_2888,
Sarcophilus harrisii	ENSSHAG00000017422	1 retrocopy	retro_shar_343,
Sus scrofa	ENSSSCG00000024720	1 retrocopy	retro_sscr_238,