RetrogeneDB ID: retro_sscr_39

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:59934890..59935976(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000017013
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSSSCG00000030510
• Aliases: None
• Description: fibrillarin [Source:HGNC Symbol;Acc:3599]

Sequence

>retro_sscr_39
CGGCTCCCAGGTACCAGCGCCCCTGGCAACCGCTCTGAGCCGATAGAAACCCCTGCCATCCGCCGCCACCCACCCAAGCG
CCCAGGACGCACCATGAAGTCTGCAGTGAGCGCGCGCGGGGGCGGATCCGGCGGCCGCGGGGGTGGCGGCTGGGGCGGCG
GCTGGGGCGGAGGGAGAGGCGGCGGAGGAGGGGGCAAGGGAGCAGGAGGCAACAGCGGCGGCCAGGGAGGCAAGGGCGGC
TTCGGAGCGCGGACGCGAGGCTTTGGCGGCGGCCGGGGCCGGGGGCGTGGTGGCGGAGACGGCAGGGACCGCGGGGGCGG
CGGGCAGCGGCGCGGCTCTGGCAAGAGCAAGAACCGCCGCAGGAAGGGCGCCCACGTCGTGTCGGTGGAACCGCACCGGC
ACGAGGGCGTCTTCATCTACCGCGGGGCGGAGGATGCGCTGGTCACGCTGAACATGGTGCCAGGCCAGTCGGTATACGGT
GAGCGGCGGGTCACGGTGACCGAGGGTGGCGTGAAACAGGAGTACCGCACGTGGAACCCGTTCCGCTCCAAGCTGGCCGC
GGCCATACTGGGCGGGGTCGACCAGATTCACATCAAGCCCAAGTCCAAAGTCCTGTACCTGGGTGCTGCCTCGGGGACCA
CGGTCTCCCACGTCTCCGACATCATCGGCCCGGATGGCCTGGTCTACGCGGTCGAGTTTTCCCACCGCGCCGGCCGCGAT
CTCGTCAATGTGGCCAAGAAGCGAACCAACATCATCCCGGTCCTTGAAGATGCCCGGCACCCACTCAAGTATCGCATGTT
AATTGGGATGGTGGACGTGATCTTTGCTGACGTGGCCCAGCCAGACCAGTCCCGCATCGTGGCTCTGAATGCCCACACCT
TCCTGCGCAATGGGGGCCACTTCCTCATTTCCATCAAAGCCAACTGCATCGACTCCACCGCATCTGCCGAGGCGGTGTTT
GCCTCTGAAGTGAAGAAGTTGCAGCAGGAGAATTTAAAGCCTCAAGAGCAGCTGACCCTGGAGCCCTATGAGAGGGACCA
CGCTGTGGTCGTTGGGGTCTATCGGCCCCTTCCCAAGAGTGGCAGC

Alignment

ORF - retro_sscr_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.49 %
• Parental protein coverage: 88.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGGFGGRGGFGDRGGRGGGRGGFGGGRGGFGGGRGRGGGFRGRGRGGGGG-GRGGGFQSGGSRGRGRGGK
          GGG.GG..G.G..G...GG..G..GG.GGFG......GG.RGRGRGGG.G..RGGG...G..RG.G....
Retrocopy GGGWGGGRGGGGGGKGAGGNSGGQGGKGGFGARTRGFGGGRGRGRGGGDGRDRGGG---GQRRGSGKSKN

Parental  KGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAA
          ........V.VEPHRHEGVFI.RG.EDALVT.N.VPG.SVYGE.RV...EG..K.EYR.WNPFRSKLAAA
Retrocopy RRRKGAHVVSVEPHRHEGVFIYRGAEDALVTLNMVPGQSVYGERRVTVTEGGVKQEYRTWNPFRSKLAAA

Parental  ILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDA
          ILGGVDQIHIKP..KVLYLGAASGTTVSHVSDI.GPDGLVYAVEFSHR.GRDL.N.AKKRTNIIPV.EDA
Retrocopy ILGGVDQIHIKPKSKVLYLGAASGTTVSHVSDIIGPDGLVYAVEFSHRAGRDLVNVAKKRTNIIPVLEDA

Parental  RHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQ
          RHP.KYRMLI.MVDVIFADVAQPDQ.RIVALNAHTFLRNGGHF.ISIKANCIDSTASAEAVFASEVKK.Q
Retrocopy RHPLKYRMLIGMVDVIFADVAQPDQSRIVALNAHTFLRNGGHFLISIKANCIDSTASAEAVFASEVKKLQ

Parental  QENMKPQEQLTLEPYERDHAVVVGVYRPPPK
          QEN.KPQEQLTLEPYERDHAVVVGVYRP.PK
Retrocopy QENLKPQEQLTLEPYERDHAVVVGVYRPLPK

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
SRP014902_placenta	0.13 RPM	50.97 RPM
SRP014902_testis	0.28 RPM	90.53 RPM
SRP018288_heart	0.00 RPM	19.17 RPM
SRP018288_kidney	0.00 RPM	27.88 RPM
SRP018288_liver	0.00 RPM	35.66 RPM
SRP018288_lung	0.00 RPM	35.13 RPM
SRP018856_adipose	0.18 RPM	52.68 RPM
SRP035408_brain	17.06 RPM	50.94 RPM
SRP035408_liver	0.00 RPM	45.50 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_39 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_39 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_39 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
Canis familiaris	retro_cfam_1697
Equus caballus	retro_ecab_308

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002579	1 retrocopy	retro_btau_108,
Canis familiaris	ENSCAFG00000005412	1 retrocopy	retro_cfam_1697,
Homo sapiens	ENSG00000105202	1 retrocopy	retro_hsap_99,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Microcebus murinus	ENSMICG00000007686	1 retrocopy	retro_mmur_1127,
Mus musculus	ENSMUSG00000046865	4 retrocopies	retro_mmus_1141, retro_mmus_1585, retro_mmus_1609, retro_mmus_89,
Nomascus leucogenys	ENSNLEG00000014234	1 retrocopy	retro_nleu_1947,
Otolemur garnettii	ENSOGAG00000006463	2 retrocopies	retro_ogar_3102, retro_ogar_504,
Pan troglodytes	ENSPTRG00000010982	2 retrocopies	retro_ptro_2208, retro_ptro_3074,
Pteropus vampyrus	ENSPVAG00000010849	1 retrocopy	retro_pvam_231,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sus scrofa	ENSSSCG00000030510	1 retrocopy	retro_sscr_39 ,
Tupaia belangeri	ENSTBEG00000007755	2 retrocopies	retro_tbel_3774, retro_tbel_3974,