RetrogeneDB ID: retro_ecab_308

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:12391870..12392564(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000023600
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSECAG00000023221
• Aliases: None
• Description: fibrillarin [Source:HGNC Symbol;Acc:3599]

Sequence

>retro_ecab_308
GTGGAGCCGCACCGGCACGAGGGCGTCTTCATCTACCGCGGGGCGGAAGGACGCTCTGGTCACGCTGAACATGGTGCCCG
GCCACTCGGTGTACGGCGAGCGGCGGGTCACGGTGACCGAGGGCGGCGTCAAGCAGGAGTACCGCACGTGGAACCCCTTC
CGCTCCAAGCTGGCTGCGGCCATCCTGGGCGGAGTCGACCAGATCCACATCAAGCCCAAGTCCAAAGTGCTGTATCTGGG
CGCCGCCTCGGGGACCACTGTCTCCCACGTCTCTGACATCATCGGCCCCGACGGGCTGGTCTACGCGGTCGAGTTCTCCC
ACCGCGCTGGCCGCGATCTGGTCAACGTGGCCAAGAAGCGAACCAACATCATCCCAGTCCTCGAAGATGCCCGGCACCCG
CTCAAGTACCGCATGCTCATTGGGATGGTGGACGTGATCTTCGCCGACGTCGCCCAGCCGGACCAGTCCCGCATCGTGGC
TCTGAACGCCCACACCTTCCTGCGCAACGGGGGCCACTTCCTCATTTCCATCAAGGCCAACTGCATCGACTCGACTGCGT
CTGCCGAGGCGGTGTTTGCTTCTGAGGTGAGGAAGTTGCAGCAGGAGAACTTAAAGCCCCAGGAGCAGCTGACACTGGAG
CCCTATGAGCGGGACCACGCGGTGGTCGTCGGGGTCTACCGGCCGCTTCCCAAG

Alignment

ORF - retro_ecab_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 73.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEPHRHEGVFICRGKE-DALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQIH
          VEPHRHEGVFI.RG.E.DALVT.N.VPG.SVYGE.RV...EG..K.EYR.WNPFRSKLAAAILGGVDQIH
Retrocopy VEPHRHEGVFIYRGAE>DALVTLNMVPGHSVYGERRVTVTEGGVKQEYRTWNPFRSKLAAAILGGVDQIH

Parental  IKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRML
          IKP..KVLYLGAASGTTVSHVSDI.GPDGLVYAVEFSHR.GRDL.N.AKKRTNIIPV.EDARHP.KYRML
Retrocopy IKPKSKVLYLGAASGTTVSHVSDIIGPDGLVYAVEFSHRAGRDLVNVAKKRTNIIPVLEDARHPLKYRML

Parental  IAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQ
          I.MVDVIFADVAQPDQ.RIVALNAHTFLRNGGHF.ISIKANCIDSTASAEAVFASEV.K.QQEN.KPQEQ
Retrocopy IGMVDVIFADVAQPDQSRIVALNAHTFLRNGGHFLISIKANCIDSTASAEAVFASEVRKLQQENLKPQEQ

Parental  LTLEPYERDHAVVVGVYRPPPK
          LTLEPYERDHAVVVGVYRP.PK
Retrocopy LTLEPYERDHAVVVGVYRPLPK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	88.84 RPM
SRP021940_cerebellum	18.33 RPM	53.18 RPM
SRP021940_embryo	4.22 RPM	130.93 RPM
SRP021940_placental_villous	0.00 RPM	55.38 RPM
SRP021940_synovial_membrane	0.03 RPM	94.79 RPM
SRP021940_testis	3.84 RPM	98.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_308 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_308 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_99
Pan troglodytes	retro_ptro_2208
Bos taurus	retro_btau_108
Sus scrofa	retro_sscr_39
Canis familiaris	retro_cfam_1697

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023221	1 retrocopy	retro_ecab_308 ,
Loxodonta africana	ENSLAFG00000000171	1 retrocopy	retro_lafr_23,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sorex araneus	ENSSARG00000008709	1 retrocopy	retro_sara_768,
Ictidomys tridecemlineatus	ENSSTOG00000012486	1 retrocopy	retro_itri_1302,
Tursiops truncatus	ENSTTRG00000003967	1 retrocopy	retro_ttru_30,