RetrogeneDB ID: retro_sscr_149

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:309568432..309569218(+)
• Located in intron of: None

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_149
ATGGGCTTTGTAAAAGTTGTCAAGAATAAGGGCTTCATCAAGAGGTATCAAGTGAAATCTAGAAGAAGACAAGAGGGTAA
AACTGACTACTATGCTGGGAAATGATTGGTCATCCAAGATAAAAAATAAGTACAACACACCCGAATACGGGAGTTAGTTT
GTGTAACCAACAGAGATATCATTTGTCAGATTGCTTATGCTTGTATAGGAGATATGATAGTTTGTGCAGCTCATACTCAC
CAACTCCCAAACTATGGTGCGAGGATTGGCCTGACAAATCATGCTGCAGCATATTGTACTGACTTGCTGCTGGCCCGCAA
GCTTCTTAATAGATTTAGTATGGACCACATATGTGAAGGCCAGGTTGAGGTGACTGGAGATGAATACAATATGGAAAACA
TTGATAGTCAACCTGGTAACTTCACCTGTTATTTGGATGCAGGGCTTGCCAGGACTACTACTGGAAACAAAGTTTTTGGG
GCCCTGAATTGAGCTGTAGATGGAGGCTTGTCTATCCTTCACAGTACCAAATGATAACCTTGTTATGATTCAGAAAGCAA
AGAATTCAAGGCTGAGATACACCGAAAGCACATCATGGGGCAGAACGTTGTAGATTACATGCTTTACCTGACTGAAGAAG
ATGAGGTTGCTTAGGAGAAACTGTTCTCTCAATACATAAAGAATAAAAGTAACTCCAGACATGGAAAAATGTTTACGAAA
GCTCATGCGGCAATACGAGAGAATCCAGCGTATAAGGAGCAGCCTAAGAAAGAAAGAAGTGAAAAA

Alignment

ORF - retro_sscr_149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.49 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDK-NKYNTPKY-RMIVRVTNRDIICQIAYAR
          MGFVKVVKNK...KRYQVK.RRR.EGKTDYYA.K.LVIQDK.NKYNTP.Y.R..V.VTNRDIICQIAYA.
Retrocopy MGFVKVVKNKGFIKRYQVKSRRRQEGKTDYYAGK*LVIQDK>NKYNTPEY<RELVCVTNRDIICQIAYAC

Parental  IEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQ
          I.GDMIVCAA..H.LP.YG...GLTN.AAAYCT.LLLAR.LLNRF.MD.I.EGQVEVTGDEYN.E.ID.Q
Retrocopy I-GDMIVCAAHTHQLPNYGARIGLTNHAAAYCTDLLLARKLLNRFSMDHICEGQVEVTGDEYNMENIDSQ

Parental  PGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHILGQNVADYM
          PG.FTCYLDAGLARTTTGNKVFGAL..AVDGGLSI.HSTK..P.YDSESKEF.AE.HRKHI.GQNV.DYM
Retrocopy PGNFTCYLDAGLARTTTGNKVFGALN*AVDGGLSILHSTK**PCYDSESKEFKAEIHRKHIMGQNVVDYM

Parental  RYLIEEDEDAYKKQFSQYIKN-NVTPDMMEEMYKK-AHAAIRENPVYEKKPKKEVKKK
          .YL.EEDE.A..K.FSQYIKN..VTPD.ME....K.AHAAIRENP.Y...PKKE...K
Retrocopy LYLTEEDEVA*EKLFSQYIKN>KVTPD-MEKCLRK<AHAAIRENPAYKEQPKKERSEK

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	0.00 RPM	1152.79 RPM
SRP018288_heart	0.00 RPM	774.07 RPM
SRP018288_kidney	0.00 RPM	642.85 RPM
SRP018288_liver	0.00 RPM	568.16 RPM
SRP018288_lung	0.10 RPM	913.38 RPM
SRP018856_adipose	0.00 RPM	2066.13 RPM
SRP035408_brain	0.00 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_149 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_149 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_149 has 0 orthologous retrocopies within eutheria group .

---

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,