RetrogeneDB ID: retro_sscr_169

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:119675773..119677147(-)
• Located in intron of: ENSSSCG00000029654

Retrocopy information

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

Parental gene information

• Parental gene symbol: EF1ALPHA
• Ensembl ID: ENSSSCG00000004489
• Aliases: EEF1A1, EF1A1
• Description: Sus scrofa eukaryotic translation elongation factor 1 alpha 1 (EEF1A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001097418]

Sequence

>retro_sscr_169
GGAAAGGAGAAGATTCATATCAATGTTATTGTCATTGGACATGTAGTTTGAGAAAGTCTACCACTACTGGCCATCTGATC
TACAAATGTGGTGAGATCAACAAAAGGACCGTCAAAAAGTTTGAGGAGGAGGCTGCTGAGATTGCAAAGGGTTCCAAGTA
TGCCTGGGTCTTGGACAAACTGAAAGTTGAACCTGAGTGTGTTATTTCCATTGATATCTCCCTGTAGAAATTAAAGACCA
GCAAGTACTATGTGACCATCGTTGATGCCCCAGGACACAGAGACTTATTAAAAGCATGATTACAGGCACATCCCGGGATG
GTTGTCGTTTCCTGATTATTGCTGCTGGTGTTGGTGAATTTGAAGCAAGTATCTCCAAGAATGAGCTGATCCATGAGCAT
GCCCTTCTGGCTTACACTCTGGGTGTGAAACAACTAACTGTTGGAATTAACCAAGTGGATTCCACTGAGCCCCCCAACAG
CCAAAAGAGCTGAGAGGAAATTGTTAAGGAAGTTAGCACCTATATTTTTTAAAAAGTGGCTATAATCTCAACACAGTAGC
ATTTGTGCCAATTTTTGGCTGGAATGGTGACAACATGCTGAAGCCAAGTGCTGACATGCCTTGGTTCAAGGGATGGAAAT
TCACCCATAAAATGGCAATGCCGGTAGAACCATGTTGTTTGAAGCTCTGGATTGCATCTTGCCACCAACTTGTCCAACTG
ACAAACCCTGTGTCTGCCCCTCTAGAACGTCTACAAAATTGGTGGCATGGATACTGTCCATGGGTGCAATGTAGACTGGC
ATTCTCAAATCTGGCATGATGGTCACCTTTGCTCCAGTCAATGTTACAAATGAAGTCAAGTCTGTTGAAATGCACATGAA
GCTTTGAGTGAAGCCCTTTCCAGGGACAATGAGGGCTTCAGTGTCAGGAATGTGTCTGTCAAACATGTTCATCATGGCAG
TATGGCTGATATCAAAAAAATGACCCACCAAAGGAAGCAGCTGGCCTTACAGCTCAGGTGATTATCTTGAACCATCCTGG
TCAAATCAGTGCTAGATATGTACCTGTGCTGGATTGTCTCACAGCTCAAATTGCTTGCAAGTTTGCTGAACTGAAGAAGA
TTGATCATCATTCTGGGAAAAAGCTGGGAGATGGCCCCAAATTCTTGAACTCTGGTGATGCTACCATTGTTGATAGGGTT
CCTGGTAAGCCCATGTGTGTTGAGAGTTTCTCTGACTATCCTCCCCTGAGCCGTTTTGCTCTTCATGACATGAGACAGAT
GGTGGTCACTGTGGTTTTCATCAAAGCAGTGAACAAAAAGGCAGCTGGAGCTGGCAAGGTCACCAAGTCTGCTCAGAAAG
CTCAGAAATCTAAA

Alignment

ORF - retro_sscr_169 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.25 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  GKEKTHINIVVIGHV-DSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
          GKEK.HIN..VIGHV....KSTTTGHLIYKCG.I.KRT..KFE.EAAE..KGS.KYAWVLDKLK.E.E..
Retrocopy GKEKIHINVIVIGHV<SLRKSTTTGHLIYKCGEINKRTVKKFEEEAAEIAKGS-KYAWVLDKLKVEPECV

Parental  ITIDISLWKFETSKYYVTIIDAPGHRDF-IKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
          I.IDISL.K..TSKYYVTI.DAPGHRD..IK.MITGTS...C..LI.AAGVGEFEA.ISKN....EHALL
Retrocopy ISIDISL*KLKTSKYYVTIVDAPGHRDL<IKSMITGTSRDGCRFLIIAAGVGEFEASISKNELIHEHALL

Parental  AYTLGVKQLIVGVNKMDSTEP-PYSQKRYEEIVKEVST-YIKKIGYNPDTVAFVPISGWNGDNMLEPSAN
          AYTLGVKQL.VG.N..DSTEP.P................Y..K.GYN..TVAFVPI.GWNGDNML.PSA.
Retrocopy AYTLGVKQLTVGINQVDSTEP>PTAKRAERKLLRKLAP>YFLKSGYNLNTVAFVPIFGWNGDNMLKPSAD

Parental  MPWFKGWKVTRK-DGNASGTTLLEALDCILPPTRPTDKP-LRLPLQDVYKIGGI-GTVP-VGRVETGVLK
          MPWFKGWK.T.K..GNA..T.L.EALDCILPPT.PTDKP.L.LPL..VYKIGG..G..P..G...TG.LK
Retrocopy MPWFKGWKFTHK<NGNAGRTMLFEALDCILPPTCPTDKP<LCLPL*NVYKIGGM<GYCP<MGAM*TGILK

Parental  PGMVVTFAPVNVTTEVKSVEMH-HEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSK-NDPPMEAAGFT
          .GM.VTFAPVNVT.EVKSVEMH.HEALSEAL..DN.GF.V.NVSVK.V..G..A...K.NDPP.EAAG.T
Retrocopy SGMMVTFAPVNVTNEVKSVEMH<HEALSEALSRDNEGFSVRNVSVKHVHHGSMADIKK<NDPPKEAAGLT

Parental  AQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMC
          AQVIILNHPGQISA.Y.PVLDC.TA.IACKFAELK.KID..SGKKL.DGPKFL.SGDA.IVD.VPGKPMC
Retrocopy AQVIILNHPGQISARYVPVLDCLTAQIACKFAELK-KIDHHSGKKLGDGPKFLNSGDATIVDRVPGKPMC

Parental  VESFSDYPPLGRFAVRDMRQ-TVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          VESFSDYPPL.RFA..DMRQ..V.V..IKAV.KKAAGAGKVTKSAQKAQK.K
Retrocopy VESFSDYPPLSRFALHDMRQMVVTVVFIKAVNKKAAGAGKVTKSAQKAQKSK

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	11400.80 RPM
SRP014902_testis	0.71 RPM	9042.38 RPM
SRP018288_heart	0.00 RPM	2428.25 RPM
SRP018288_kidney	0.00 RPM	5194.10 RPM
SRP018288_liver	0.00 RPM	3692.15 RPM
SRP018288_lung	0.00 RPM	6639.68 RPM
SRP018856_adipose	0.23 RPM	25927.80 RPM
SRP035408_brain	0.06 RPM	3538.43 RPM
SRP035408_liver	0.00 RPM	3777.12 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_169 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_169 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 126 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014534	3 retrocopies	retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000020363	2 retrocopies	retro_ecab_66, retro_ecab_93,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Felis catus	ENSFCAG00000030977	14 retrocopies	retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683, retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Homo sapiens	ENSG00000156508	27 retrocopies	retro_hsap_1093, retro_hsap_1181, retro_hsap_1567, retro_hsap_1671, retro_hsap_190, retro_hsap_2302, retro_hsap_2455, retro_hsap_2637, retro_hsap_2712, retro_hsap_278, retro_hsap_283, retro_hsap_2896, retro_hsap_2920, retro_hsap_2967, retro_hsap_2983, retro_hsap_3239, retro_hsap_3291, retro_hsap_3314, retro_hsap_363, retro_hsap_3701, retro_hsap_3706, retro_hsap_3758, retro_hsap_3825, retro_hsap_3917, retro_hsap_4220, retro_hsap_4730, retro_hsap_989,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Myotis lucifugus	ENSMLUG00000013537	24 retrocopies	retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furo	ENSMPUG00000003816	6 retrocopies	retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furo	ENSMPUG00000004271	10 retrocopies	retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Oryctolagus cuniculus	ENSOCUG00000008481	3 retrocopies	retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Ochotona princeps	ENSOPRG00000016685	6 retrocopies	retro_opri_1049, retro_opri_1076, retro_opri_1197, retro_opri_298, retro_opri_325, retro_opri_383,
Sus scrofa	ENSSSCG00000004489	4 retrocopies	retro_sscr_169 , retro_sscr_492, retro_sscr_612, retro_sscr_758,
Tursiops truncatus	ENSTTRG00000000114	19 retrocopies	retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,