RetrogeneDB ID: retro_sscr_219

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:29235946..29236395(+)
• Located in intron of: ENSSSCG00000010931

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000006899
• Aliases: None
• Description: Sus scrofa ribosomal protein L5 (RPL5), mRNA. [Source:RefSeq mRNA;Acc:NM_001114284]

Sequence

>retro_sscr_219
ACCTGTTATTTGGATGCCAGGACGACTACAGGAAATAAAGTTTTGGGGGCCCTGAAGGGGGCTGTAGATGTAGGCACATC
CATCCCTTACTGTACCAAACAGTTACCTGGTTGTGACTCAGAAAAGCAAAGAATTCAATACTCAGGTATACCAAGAGCAC
ATCACGGGGTAGAACGTTGCAGATTTTATGTGTTACCTGACTGAAGAAGATGAGGATGCTTATAAGAAACAGGTCTCTCA
ATATATAAAGAACATAACTCCAGATGTGATGGAGGAAATGGATAAGAAATGTTGCAATACAAAAGAATCCAGTGTATGAA
AAGAAGCCCAAGAAAGAAGTTAAAAAGAAGAGGTGGACTCGTCCCAAAATGTCACTTGCCCAGAAGAAAGATCAGCAGCT
GGCTCAGAGGAAGGCAAGCTTCCTTAGAGCTCAGGAATGGGTTGCTGAG

Alignment

ORF - retro_sscr_219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.77 %
• Parental protein coverage: 51.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSE-SKEFNAEVHRKHILGQNVADYMRYL
          TCYLD...ARTTTGNKV.GALKGAVD.G.SIP..TK..PG.DSE.SKEFN..V...HI.G.NVAD.M.YL
Retrocopy TCYLD---ARTTTGNKVLGALKGAVDVGTSIPYCTKQLPGCDSE>SKEFNTQVYQEHITG*NVADFMCYL

Parental  IEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVA
          .EEDEDAYKKQ.SQYIK.N.TPD.MEEM.KK......E..V.........K...................
Retrocopy TEEDEDAYKKQVSQYIK-NITPDVMEEMDKKC-CNTKESSV*KEAQERS*KEEVDSSQNVTCPEERSAAG

Parental  QKK-ASFLRAQERAAE
          ....ASFLRAQE..AE
Retrocopy SEE>ASFLRAQEWVAE

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	0.00 RPM	540.88 RPM
SRP014902_testis	0.14 RPM	1152.79 RPM
SRP018288_heart	0.08 RPM	774.07 RPM
SRP018288_kidney	0.10 RPM	642.85 RPM
SRP018288_liver	0.00 RPM	568.16 RPM
SRP018288_lung	0.00 RPM	913.38 RPM
SRP018856_adipose	0.03 RPM	2066.13 RPM
SRP035408_brain	0.06 RPM	944.40 RPM
SRP035408_liver	0.00 RPM	942.58 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_219 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_219 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009878	5 retrocopies	retro_amel_1200, retro_amel_137, retro_amel_139, retro_amel_1439, retro_amel_1669,
Bos taurus	ENSBTAG00000002026	2 retrocopies	retro_btau_120, retro_btau_67,
Cavia porcellus	ENSCPOG00000000698	8 retrocopies	retro_cpor_1047, retro_cpor_1097, retro_cpor_1141, retro_cpor_1259, retro_cpor_1354, retro_cpor_1387, retro_cpor_428, retro_cpor_737,
Dipodomys ordii	ENSDORG00000005674	2 retrocopies	retro_dord_226, retro_dord_670,
Equus caballus	ENSECAG00000021065	1 retrocopy	retro_ecab_654,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Mustela putorius furo	ENSMPUG00000004150	6 retrocopies	retro_mputfur_213, retro_mputfur_449, retro_mputfur_451, retro_mputfur_597, retro_mputfur_721, retro_mputfur_833,
Mus musculus	ENSMUSG00000058558	11 retrocopies	retro_mmus_1000, retro_mmus_1185, retro_mmus_1338, retro_mmus_1789, retro_mmus_1991, retro_mmus_2577, retro_mmus_2846, retro_mmus_297, retro_mmus_3076, retro_mmus_504, retro_mmus_911,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Oryctolagus cuniculus	ENSOCUG00000010089	2 retrocopies	retro_ocun_265, retro_ocun_54,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pteropus vampyrus	ENSPVAG00000015117	4 retrocopies	retro_pvam_1427, retro_pvam_355, retro_pvam_505, retro_pvam_527,
Rattus norvegicus	ENSRNOG00000023529	6 retrocopies	retro_rnor_113, retro_rnor_2246, retro_rnor_2418, retro_rnor_2498, retro_rnor_2802, retro_rnor_2922,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,
Sus scrofa	ENSSSCG00000006899	2 retrocopies	retro_sscr_149, retro_sscr_219 ,
Tupaia belangeri	ENSTBEG00000010560	5 retrocopies	retro_tbel_101, retro_tbel_1054, retro_tbel_1518, retro_tbel_3006, retro_tbel_3530,
Tursiops truncatus	ENSTTRG00000013097	5 retrocopies	retro_ttru_1446, retro_ttru_1548, retro_ttru_1796, retro_ttru_645, retro_ttru_979,