RetrogeneDB ID: retro_sscr_116

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:92577660..92578123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL24
• Ensembl ID: ENSSSCG00000011952
• Aliases: None
• Description: ribosomal protein L24 [Source:HGNC Symbol;Acc:10325]

Sequence

>retro_sscr_116
AAGGTTGAGCTTTGCTATTTCAGCAGGTACAAGATCCACCCAGGTCATGGGAGGTGCTACAACAGAACTAATGGGAAGGT
TTTCCAAGTTCTTAATGCAAAATATAAGTGTGCATTCCTTTCCACAAGGAATCCTCGGAGACCAACTGGACTGTTCTTTA
CAGAAGGAAGCACAAACAGAGACAGTTGGAAGAAATTCGAAAGAAAAGAACCCGCCATGTAGTCAGATTCCGGAGTGCCA
TAATTAGTGCATCACTTGCTGATATAATGGCCAAGAGGAATCAGAAACCTGAAGTTAAAAAGGCTAAAGACAACAAGCTA
TCAGGGCTGCCAAGGAAACAAAAAAGGCTAAGCAAGTATCTAAAAAGACAGCAAAGGCTGCTGTGAAGGCTCCCACAAAG
GCAATACCTAAGCAAAGGATTGTGAAGCCTGTGAAGGTTTCTGCTCCCCAAGTTGGTAGAAAA

Alignment

ORF - retro_sscr_116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.8 %
• Parental protein coverage: 98.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPR-QINWTVLYRRKHKKGQSEEIQKK
          .VELC.FS.YKI.PGHGR.Y.RT.GKVFQ.LNAK...AFLS.RNPR...NWTVLYRRKHK..Q.EEI.KK
Retrocopy KVELCYFSRYKIHPGHGRCYNRTNGKVFQVLNAKYKCAFLSTRNPR<ETNWTVLYRRKHKQRQLEEIRKK

Parental  RTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQ-REQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPK
          RTR..V.F..AI..ASLADIMAKRNQKPEV.KA..R.QAIRAAKE.KKAKQ.SKKTA.AA.KAPTKA.PK
Retrocopy RTRHVVRFRSAIISASLADIMAKRNQKPEVKKAK<RQQAIRAAKETKKAKQVSKKTAKAAVKAPTKAIPK

Parental  QKIVKPVKVSAPRVGGK
          Q.IVKPVKVSAP.VG.K
Retrocopy QRIVKPVKVSAPQVGRK

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	116.94 RPM
SRP014902_testis	0.00 RPM	261.53 RPM
SRP018288_heart	0.03 RPM	378.03 RPM
SRP018288_kidney	0.00 RPM	259.66 RPM
SRP018288_liver	0.00 RPM	253.14 RPM
SRP018288_lung	0.00 RPM	125.86 RPM
SRP018856_adipose	0.00 RPM	641.12 RPM
SRP035408_brain	0.00 RPM	778.39 RPM
SRP035408_liver	0.00 RPM	645.83 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_116 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 106 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003740	3 retrocopies	retro_amel_1042, retro_amel_1089, retro_amel_201,
Canis familiaris	ENSCAFG00000009601	4 retrocopies	retro_cfam_1908, retro_cfam_615, retro_cfam_862, retro_cfam_989,
Callithrix jacchus	ENSCJAG00000000496	3 retrocopies	retro_cjac_2544, retro_cjac_2941, retro_cjac_327,
Cavia porcellus	ENSCPOG00000019941	5 retrocopies	retro_cpor_1020, retro_cpor_461, retro_cpor_474, retro_cpor_904, retro_cpor_947,
Dasypus novemcinctus	ENSDNOG00000003194	9 retrocopies	retro_dnov_1209, retro_dnov_1259, retro_dnov_1449, retro_dnov_1643, retro_dnov_2191, retro_dnov_2407, retro_dnov_2537, retro_dnov_523, retro_dnov_657,
Equus caballus	ENSECAG00000024095	1 retrocopy	retro_ecab_205,
Felis catus	ENSFCAG00000003327	1 retrocopy	retro_fcat_31,
Loxodonta africana	ENSLAFG00000013804	3 retrocopies	retro_lafr_181, retro_lafr_452, retro_lafr_612,
Macropus eugenii	ENSMEUG00000009177	7 retrocopies	retro_meug_1769, retro_meug_371, retro_meug_385, retro_meug_449, retro_meug_730, retro_meug_759, retro_meug_963,
Myotis lucifugus	ENSMLUG00000017005	4 retrocopies	retro_mluc_1990, retro_mluc_2185, retro_mluc_35, retro_mluc_393,
Macaca mulatta	ENSMMUG00000015059	9 retrocopies	retro_mmul_1234, retro_mmul_1711, retro_mmul_1803, retro_mmul_2263, retro_mmul_2521, retro_mmul_37, retro_mmul_560, retro_mmul_609, retro_mmul_823,
Monodelphis domestica	ENSMODG00000001916	3 retrocopies	retro_mdom_675, retro_mdom_854, retro_mdom_974,
Mustela putorius furo	ENSMPUG00000011738	3 retrocopies	retro_mputfur_255, retro_mputfur_406, retro_mputfur_914,
Oryctolagus cuniculus	ENSOCUG00000000791	8 retrocopies	retro_ocun_1401, retro_ocun_190, retro_ocun_303, retro_ocun_323, retro_ocun_420, retro_ocun_480, retro_ocun_526, retro_ocun_531,
Otolemur garnettii	ENSOGAG00000013843	8 retrocopies	retro_ogar_1592, retro_ogar_1777, retro_ogar_2086, retro_ogar_2785, retro_ogar_2922, retro_ogar_3356, retro_ogar_677, retro_ogar_838,
Pan troglodytes	ENSPTRG00000015176	2 retrocopies	retro_ptro_1214, retro_ptro_85,
Rattus norvegicus	ENSRNOG00000001611	25 retrocopies	retro_rnor_1244, retro_rnor_1245, retro_rnor_1247, retro_rnor_1248, retro_rnor_1250, retro_rnor_1251, retro_rnor_1252, retro_rnor_1253, retro_rnor_1452, retro_rnor_1643, retro_rnor_1699, retro_rnor_1850, retro_rnor_1851, retro_rnor_1985, retro_rnor_2026, retro_rnor_2134, retro_rnor_2148, retro_rnor_2205, retro_rnor_2214, retro_rnor_2294, retro_rnor_2709, retro_rnor_435, retro_rnor_751, retro_rnor_964, retro_rnor_993,
Sarcophilus harrisii	ENSSHAG00000008226	2 retrocopies	retro_shar_171, retro_shar_264,
Sus scrofa	ENSSSCG00000011952	4 retrocopies	retro_sscr_116 , retro_sscr_1218, retro_sscr_669, retro_sscr_932,
Ictidomys tridecemlineatus	ENSSTOG00000014654	2 retrocopies	retro_itri_442, retro_itri_69,