RetrogeneDB ID: retro_pcap_326

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_38153:12041..12453(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF2
• Ensembl ID: ENSPCAG00000001026
• Aliases: None
• Description: myeloid leukemia factor 2 [Source:HGNC Symbol;Acc:7126]

Sequence

>retro_pcap_326
CAGCCATGGGCTGTCTCCCACTTTGTGATGCTGGCAATGTTGGGTGGCTTCCCTGGACATGCTTGGGATGATGAACGACA
AGACTGGGAACGCAGGGCACACGACAGCTGGAGGCAATTGCCAGACCTTTCCATGCTCCACTGTGATCTATTTCAACACA
GGACATGGTGCCCCGCGTTCTACCGAGAGACTCTGGAGATGTGATCAGCACTTGGTGGATATGGGAGACACTGAGGACTG
TGAGGGACCTGGACTATGCATTAGAGCAGATGTTCAGTGGGCATCAGTTAGCAGACAGGGCTTACATCCTATAGTGCCCC
CAAACCACCTTACGGGGGGACAGGAAGAGCCGCAGTATGACATCAATTTGGGCAAGAGTGAGACCGCAGCATTTGATGGC
GAGCAGCGGAGA

Alignment

ORF - retro_pcap_326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.44 %
• Parental protein coverage: 55.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QAGAVSPFGMLGMSGGF-MDMFGMMNDMIGNMEHMTAGGNCQTFSSSTVISYSNTGDGAPK-VYQETSKM
          Q..AVS.F.ML.M.GGF..DM.GMMND..GN..H.TAGGNCQTF..STVI.Y.NTG.GAP...Y.ET..M
Retrocopy QPWAVSHFVMLAMLGGF>LDMLGMMNDKTGNAGHTTAGGNCQTFPCSTVI-YFNTGHGAPR<FYRETLEM

Parental  RSAPCG-IRETRRTVRDSDSGLEQMSIGHHIRDRAHILQRSRNHRTGD-QEERQDYINLDESEAAAFNDE
          .SA..G.I.ET.RTVRD.D..LEQM..GH...DRA.IL........GD.QEE.Q..INL..SE.AAF..E
Retrocopy *SALGG<IWETLRTVRDLDYALEQMFSGHQLADRAYIL*CPQTTLRGD<QEEPQYDINLGKSETAAFDGE

Parental  WRR
          .RR
Retrocopy QRR

Legend:

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

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_326 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000758	2 retrocopies	retro_dnov_1602, retro_dnov_649,
Echinops telfairi	ENSETEG00000014471	2 retrocopies	retro_etel_1236, retro_etel_233,
Microcebus murinus	ENSMICG00000010652	1 retrocopy	retro_mmur_449,
Monodelphis domestica	ENSMODG00000018113	1 retrocopy	retro_mdom_324,
Mus musculus	ENSMUSG00000030120	1 retrocopy	retro_mmus_1090,
Otolemur garnettii	ENSOGAG00000005976	1 retrocopy	retro_ogar_232,
Procavia capensis	ENSPCAG00000001026	1 retrocopy	retro_pcap_326 ,
Ictidomys tridecemlineatus	ENSSTOG00000009908	1 retrocopy	retro_itri_1707,