RetrogeneDB ID: retro_sscr_1204

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:78698219..78698678(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030962
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF5A
• Ensembl ID: ENSSSCG00000017939
• Aliases: None
• Description: eukaryotic translation initiation factor 5A [Source:HGNC Symbol;Acc:3300]

Sequence

>retro_sscr_1204
ATGGCAGTTGATTTGGACTTTGAGACAGGAGATGCAGGAGCCTCAGCCACCTTCCCACTGCAGTGCTCATTACTACATAA
GAATGGTTTTGTGGTGCTCACAGGCTGGCCATGTAAGATTGTGTAAGTATTGACCTCCAAAACTGGAAAGCATGGCCACA
CCAAGGTCCATGTGGTTGGTAATGATATCTTTGTTAGGAAGAAATATGAAGATATCTGCCCGTCAACTCAGAATTTGGTT
GTCCCCAACATGAAAAGGAGGGATTGCCAGCTGATTGGCATCCAGGATAGGTCTCTATCACTGCCCCAAGGTAGCGGGGA
GATTCCAGAGAACCTTTGTCCACCTGAGGGAGACCTTAGAAAGGAGATTGAGCAGAAGTATGAATGTGAAGAGATTCTGA
TCACAGTACTGTTTGCTTTGACAGAGGAGGCAGGTGTTGCAATCAAGGACATGGCAAAA

Alignment

ORF - retro_sscr_1204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADDLDFETGDAGASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYE
          MA.DLDFETGDAGASATFP.QCS.L.KNGFVVL.G.PCKIV...TSKTGKHGH.KVH.VG.DIF..KKYE
Retrocopy MAVDLDFETGDAGASATFPLQCSLLHKNGFVVLTGWPCKIV*VLTSKTGKHGHTKVHVVGNDIFVRKKYE

Parental  DICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSA
          DICPST.N..VPN.KR.D.QLIGIQD..LSL.Q.SGE..E.L..PEGDL.KEIEQKY.C.EEILITVL.A
Retrocopy DICPSTQNLVVPNMKRRDCQLIGIQDRSLSLPQGSGEIPENLCPPEGDLRKEIEQKYEC-EEILITVLFA

Parental  MTEEAAVAIKAMAK
          .TEEA.VAIK.MAK
Retrocopy LTEEAGVAIKDMAK

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	498.80 RPM
SRP014902_testis	0.00 RPM	382.90 RPM
SRP018288_heart	0.00 RPM	108.49 RPM
SRP018288_kidney	0.00 RPM	259.76 RPM
SRP018288_liver	0.00 RPM	374.67 RPM
SRP018288_lung	0.00 RPM	290.00 RPM
SRP018856_adipose	0.00 RPM	293.88 RPM
SRP035408_brain	0.00 RPM	153.47 RPM
SRP035408_liver	0.00 RPM	185.50 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1204 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132507	3 retrocopies	retro_hsap_1788, retro_hsap_2004, retro_hsap_9,
Gorilla gorilla	ENSGGOG00000012032	2 retrocopies	retro_ggor_1448, retro_ggor_159,
Monodelphis domestica	ENSMODG00000006652	2 retrocopies	retro_mdom_1641, retro_mdom_190,
Otolemur garnettii	ENSOGAG00000014230	1 retrocopy	retro_ogar_2414,
Pan troglodytes	ENSPTRG00000008674	3 retrocopies	retro_ptro_1198, retro_ptro_442, retro_ptro_504,
Sus scrofa	ENSSSCG00000017939	1 retrocopy	retro_sscr_1204 ,
Tursiops truncatus	ENSTTRG00000009783	1 retrocopy	retro_ttru_1526,