RetrogeneDB ID: retro_sscr_805

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:88934085..88934885(+)
• Located in intron of: ENSSSCG00000000882

Retrocopy information

• Ensembl ID: ENSSSCG00000000883
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000012178
• Aliases: None
• Description: Eukaryotic translation initiation factor 2 subunit 3 [Source:UniProtKB/TrEMBL;Acc:F1SPY4]

Sequence

>retro_sscr_805
GAGGGTAGTGTGACCCTAGGACAGCTGCATCTTTCTCTCCAGGATCTCACCACCTTGGATGTTACCAGGTTGACGCCACT
CTCACATGAAGTTATTAGCAGACAAGCCACAATTAATATAGGTACAATTGGTCATGTTGCCCATGGGAAATCTACTGTTG
TAAAAGCTATATCTGGAGTTCACACTGTTAGATTCAAAAATGAACTAGAAAGAAATATTACAATCAAGCTTGGATATGCT
AATGCCAAGATTGACAAACTTGATGATGCAAGTTGTCCTCGGCCAGAATGCTATAGACTTGTGGAAGTAGTACACCTGAT
GAGTTTCCTACAGACATTACAGGGAACTTCAAACTAGTTAGACATGTTTCCTTTGTTGACTGTCCTGATCATGATATTTT
GATGGCTACTATGCTGAATGGTGCAGCAGTGGTGGATGCAGCTCTTCTGTTAATAGCTGGTAATGAATCCTGTCCTCAAC
CTCAGACTTCTGAATACTTGGCTGCCATAGAAATTATGAAACTGAAACATATATTGATTCTACAAAATAAAATTGATTTG
GTAAAAGAAAGTCAGGCTAAAGAACAGTATGAACAGATTCTTGCATTTGTACAAGGTACAGTCACGGAAGGAGCGCCTAT
TATTCCAATTTCTGCTCAGCTGAAATATAATATTGAAGTTGTCTGTGAGTATATTGTAAAGAAAATTCCAGTATCTCTAA
GAGACTTTACTTCAGAACCTCGGCTTATTGTTATTAGGTCCTTCGATGTCAACAAACCTGGCTGTGAGGTTGATGATCTA

Alignment

ORF - retro_sscr_805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.1 %
• Parental protein coverage: 57.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EAGVTLGQPHLSRQDLTTLDVTRLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELE
          E..VTLGQ.HLS.QDLTTLDVTRLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELE
Retrocopy EGSVTLGQLHLSLQDLTTLDVTRLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELE

Parental  RNITIKLGYANAKIYKLDDASCPRPECYR-SCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMA
          RNITIKLGYANAKI.KLDDASCPRPECYR..CGSSTPDEFPTDI....GNFKLVRHVSFVDCP.HDILMA
Retrocopy RNITIKLGYANAKIDKLDDASCPRPECYR<TCGSSTPDEFPTDIT---GNFKLVRHVSFVDCPDHDILMA

Parental  TMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQG
          TMLNGAAV.DAALLLIAGNESCPQPQTSE.LAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQG
Retrocopy TMLNGAAVVDAALLLIAGNESCPQPQTSEYLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQG

Parental  TVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPLRDFTSEPRLIVIRSFDVNKPGCEVDDL
          TV.EGAPIIPISAQLKYNIEVVCEYIVKKIPV.LRDFTSEPRLIVIRSFDVNKPGCEVDDL
Retrocopy TVTEGAPIIPISAQLKYNIEVVCEYIVKKIPVSLRDFTSEPRLIVIRSFDVNKPGCEVDDL

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	0.00 RPM
SRP014902_testis	0.00 RPM	87.41 RPM
SRP018288_heart	0.00 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.00 RPM	47.29 RPM
SRP035408_liver	0.00 RPM	81.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_805 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_805 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_805 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Mus musculus	ENSMUSG00000035150	2 retrocopies	retro_mmus_1408, retro_mmus_3433,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805 ,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,