RetrogeneDB ID: retro_sscr_138

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:215499394..215500476(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL4
• Ensembl ID: ENSSSCG00000004945
• Aliases: None
• Description: ribosomal protein L4 [Source:HGNC Symbol;Acc:10353]

Sequence

>retro_sscr_138
ACTTGGGGTACTGGCAGAGCTGAGGCTCGAATTCCCAGGGTTCAAGGTGGCGGGACTCACTGTTCTGGGCAGGGTGTTTT
GGAAATATGTGTCGTGGGGGCCACATGTTTGCACCAACCAAGACCTGGCGACATTGGTACCACAGAGTGAAGGCAACACA
GAAGCGATATGCCATCTGCTCTGCACTGGCTGCCTCGGCCTTACCAGCGCTGGTCATGTCTAAAGGTCATTGGATTGAAG
AAGTTCCTGAACTACCTTTGGTGGTTGAAGATAAAGTTGAAAGTTACAAAAAGACCAAGGAGGCTGTTCTGCTTTTGAAG
AAGCTTAAGGTCTGGAATGATATCAAAAAAGGTCTATGCCTCTCAGCAAATGAGAGCTGGTAAAGGCAAAATGAGAAACC
ATCACCGTATCCAGCGCAGGGGATCCTCCATCATCTATGATGATGACAATGGTATCATCAAGGCCTTCAGAAACATCCCT
GGAATTACTCTGCTTAATGTAAGCAAACTGAACATTTTGAAACTTGCTCCTGGTGGGCATGTGGGACGTTTCTGCATTTG
GACTGAAAGTGTTTTCCGCAAGTTAGATAAGCTATGTGCACTTGGAGTAAAGCCACTTCCCTCAAGAGTAACTACAACCT
TCCCATGCATAAGATGTTCAATACAGACCTTAGCAGAATCTTGAAAAGCCCAGAGATCCAAAGAGCCCTCCATGCACCAT
GCAAGAAAATTTATCATAGAGTTTTGAAGAAGAATCCACTGAAAAACCTCAGAATCATGTTGAAGCTAAACCTGTATGCA
CAGACAATGTGCTGAAACACCATTCTTCGCCAGGCCAGGGATCGCAAAATCTGGATGAATAAGGCAGCAGCAGCACTGGA
AGCCAAATCAGGTGAGGAGGTTCCAGACAATAAGCCTGTGGTAGAGAAGAAAGGAAAGAAGGCTATTGGCAAGAAGGCTG
TTGGCGTTAAGAAGCAGAAGAAGCCTTTGGTGGGGAAAAAGGCTGTAGTGACCAAGAAACCAGAAGCTGAAAAGAAGCCT
GTGGAAAAGAAGCCTGCCACAGAAGAAAAGAAGGCTACTGCA

Alignment

ORF - retro_sscr_138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.01 %
• Parental protein coverage: 84.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SWGTGRAVARIPRVRGGGTHRSGQGA-FGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALP
          .WGTGRA.ARIPRV.GGGTH.SGQG..FGNMCRGG.MFAPTKTWR.W..RV..TQKRYAICSALAASALP
Retrocopy TWGTGRAEARIPRVQGGGTHCSGQGV<FGNMCRGGHMFAPTKTWRHWYHRVKATQKRYAICSALAASALP

Parental  ALVMSKGHRIEEVPELPLVVEDKVESYKKTKEAVLLLKKLKAWNDI-KKVYASQRMRAGKGKMRNRRRIQ
          ALVMSKGH.IEEVPELPLVVEDKVESYKKTKEAVLLLKKLK.WNDI.KKVYASQ.MRAGKGKMRN..RIQ
Retrocopy ALVMSKGHWIEEVPELPLVVEDKVESYKKTKEAVLLLKKLKVWNDI>KKVYASQQMRAGKGKMRNHHRIQ

Parental  RRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYG-TWRKAAT
          RRG..IIY..DNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTES.FRKLD.L...TW.KA..
Retrocopy RRGSSIIYDDDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESVFRKLDKLCA<TWSKATS

Parental  LKSNYNLPMHKMLNTDLSRI-KSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILR
          LKSNYNLPMHKM.NTDLSRI.KSPEIQRAL.AP.KKI..RVLKKNPLKNLRIMLKLN.YA.TM..NTILR
Retrocopy LKSNYNLPMHKMFNTDLSRILKSPEIQRALHAPCKKIYHRVLKKNPLKNLRIMLKLNLYAQTMC*NTILR

Parental  QARNHKIRMDKAAAALKAKSGEKGVPDKKPVVEKKGKKAIGKKAVGVKKQKKPLVGKKAVVTKKPAAEKK
          QAR..KI.M.KAAAAL.AKSGE..VPD.KPVVEKKG..........VKKQKKPLVGKKAVVTKKP.AEKK
Retrocopy QARDRKIWMNKAAAALEAKSGEE-VPDNKPVVEKKGXXXXXXXXXXVKKQKKPLVGKKAVVTKKPEAEKK

Parental  PAEKKPTTEEKKAVA
          P.EKKP.TEEKKA.A
Retrocopy PVEKKPATEEKKATA

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	0.27 RPM	814.04 RPM
SRP014902_testis	1.27 RPM	1369.63 RPM
SRP018288_heart	0.37 RPM	876.93 RPM
SRP018288_kidney	0.49 RPM	624.23 RPM
SRP018288_liver	0.64 RPM	601.90 RPM
SRP018288_lung	2.55 RPM	721.85 RPM
SRP018856_adipose	0.83 RPM	2256.59 RPM
SRP035408_brain	7.78 RPM	1133.37 RPM
SRP035408_liver	5.81 RPM	991.23 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_138 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_138 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_138 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005211	2 retrocopies	retro_btau_101, retro_btau_610,
Canis familiaris	ENSCAFG00000017309	1 retrocopy	retro_cfam_72,
Choloepus hoffmanni	ENSCHOG00000003008	6 retrocopies	retro_chof_1014, retro_chof_1496, retro_chof_2219, retro_chof_2616, retro_chof_455, retro_chof_476,
Callithrix jacchus	ENSCJAG00000007491	2 retrocopies	retro_cjac_251, retro_cjac_945,
Dasypus novemcinctus	ENSDNOG00000006693	3 retrocopies	retro_dnov_1028, retro_dnov_1152, retro_dnov_1931,
Equus caballus	ENSECAG00000023179	1 retrocopy	retro_ecab_428,
Echinops telfairi	ENSETEG00000000337	3 retrocopies	retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus	ENSFCAG00000012293	4 retrocopies	retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Homo sapiens	ENSG00000174444	5 retrocopies	retro_hsap_1306, retro_hsap_254, retro_hsap_2898, retro_hsap_4229, retro_hsap_471,
Gorilla gorilla	ENSGGOG00000003695	4 retrocopies	retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Loxodonta africana	ENSLAFG00000006494	3 retrocopies	retro_lafr_1076, retro_lafr_152, retro_lafr_960,
Microcebus murinus	ENSMICG00000004419	6 retrocopies	retro_mmur_1050, retro_mmur_1330, retro_mmur_440, retro_mmur_562, retro_mmur_830, retro_mmur_852,
Myotis lucifugus	ENSMLUG00000011809	2 retrocopies	retro_mluc_121, retro_mluc_198,
Macaca mulatta	ENSMMUG00000016844	2 retrocopies	retro_mmul_2160, retro_mmul_649,
Monodelphis domestica	ENSMODG00000009657	2 retrocopies	retro_mdom_656, retro_mdom_944,
Mustela putorius furo	ENSMPUG00000000337	3 retrocopies	retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Nomascus leucogenys	ENSNLEG00000012938	4 retrocopies	retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Pongo abelii	ENSPPYG00000006578	1 retrocopy	retro_pabe_152,
Pan troglodytes	ENSPTRG00000007195	6 retrocopies	retro_ptro_1512, retro_ptro_1959, retro_ptro_214, retro_ptro_2873, retro_ptro_353, retro_ptro_897,
Pteropus vampyrus	ENSPVAG00000000068	18 retrocopies	retro_pvam_1222, retro_pvam_1342, retro_pvam_201, retro_pvam_202, retro_pvam_216, retro_pvam_236, retro_pvam_267, retro_pvam_399, retro_pvam_428, retro_pvam_430, retro_pvam_435, retro_pvam_466, retro_pvam_518, retro_pvam_736, retro_pvam_778, retro_pvam_819, retro_pvam_865, retro_pvam_955,
Rattus norvegicus	ENSRNOG00000009378	5 retrocopies	retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,
Sus scrofa	ENSSSCG00000004945	2 retrocopies	retro_sscr_138 , retro_sscr_885,
Ictidomys tridecemlineatus	ENSSTOG00000009221	1 retrocopy	retro_itri_437,
Tupaia belangeri	ENSTBEG00000014392	9 retrocopies	retro_tbel_1701, retro_tbel_2186, retro_tbel_2649, retro_tbel_3302, retro_tbel_3577, retro_tbel_3624, retro_tbel_3938, retro_tbel_4340, retro_tbel_4402,
Tarsius syrichta	ENSTSYG00000005588	1 retrocopy	retro_tsyr_1144,
Tursiops truncatus	ENSTTRG00000010206	7 retrocopies	retro_ttru_1130, retro_ttru_1399, retro_ttru_1713, retro_ttru_177, retro_ttru_789, retro_ttru_817, retro_ttru_964,
Vicugna pacos	ENSVPAG00000006746	2 retrocopies	retro_vpac_143, retro_vpac_250,