RetrogeneDB ID: retro_sscr_513

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:140997254..140998151(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016241
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF2B1
• Ensembl ID: ENSSSCG00000009770
• Aliases: None
• Description: eukaryotic translation initiation factor 2B, subunit 1 alpha, 26kDa [Source:HGNC Symbol;Acc:3257]

Sequence

>retro_sscr_513
AAGTTAATTGAATACTTTACCTCTCAAATGGAAGAAGATCCTAATATGGCCTCAGCAGTAGCTGCCATCTGGACTTTGCT
GGAGTCTTGAAGAGAGATAAAGGGGAGACAATCCAGGGCCTGAGAGCGAATCTCACCAGTGCCACAGAGACCCTGTGTGG
CGTGGACTCTTCTGTGGCCGTGCCCTCCAGCAGGGAGCTCCTCCTGCGCTTCATCGGCCTTTACCTCCCTGGAATACTCT
GATTACTCCAAATGTAAAAAGATCGTGATTGAGCGGGGAGAGATTTTTCTCAGGAGAATATCACTGTCGAGAAAGACAAT
TGCAGATATGTGCCATACTTTCATCAAAGATGGGGCGAGAATACGAACTCACGCCTACTCCAGAGTGGTCCTGAGAGTCT
TGGAAGCAGCCGTGGCAGCCAAGAAGCGTTTCAGTGTATACATTACAGAGTCACAGCCTGACTTGTCAGGTAAGAAAATG
GCCAAAGCCCTCTGCCATCTCAATGTCCCCGTCCCTGTGGTCCTGGATGCTGCTGCTGGCTACATCATGGAGAAAGTGGA
TCTCGTCGTAGTTGGCGCTGAAGGAGTTGAAAACGGAGGAATGATTAACAAGGTTGGAACCAACCAGATGGCCGTATGCG
CCAAAGCACAGAACAAGCCTTTTTATGTTGTTGCAGAGTTTCAAGTTTGTACGGCTCTTCCCACTAAATCAGCAAGACGC
CCCAGGTAAGTTTAAGTACAAGGCAGATACTCTGAAGTCTGTGCAGGCCGGACAGGATCTCAAAGAGGAGCACCCATGGG
TTGACTACACCGCCCTTCCTTGATCACACTGCTCTTCAGGGACCTGGGGTTGTTGACGCCCTCTGCGGTCAGTGACGAAC
TCATCAAGCTCCATCTC

Alignment

ORF - retro_sscr_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.87 %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ELIEYFKSQMKEDPDMASAVAAIRTLLE-YLKRDKGETIQGLRANLTSAIETLCGVDSSVAVSSGGELFL
          .LIEYF.SQM.EDP.MASAVAAI.TLLE..LKRDKGETIQGLRANLTSA.ETLCGVDSSVAV.S..EL.L
Retrocopy KLIEYFTSQMEEDPNMASAVAAIWTLLE<VLKRDKGETIQGLRANLTSATETLCGVDSSVAVPSSRELLL

Parental  RFISL-TSLEYSDYSKCKKIMIERGEIFLRRISLSRKKIADMCHTFIKDGARILTHAYSRVVLRVLEAAV
          RFI.L.TSLEYSDYSKCKKI.IERGEIFLRRISLSRK.IADMCHTFIKDGARI.THAYSRVVLRVLEAAV
Retrocopy RFIGL>TSLEYSDYSKCKKIVIERGEIFLRRISLSRKTIADMCHTFIKDGARIRTHAYSRVVLRVLEAAV

Parental  AAKKRFSVYITESQPDLSGKKMAKALCHLNVPVTVVLDAAVGYIMEKVDLVIVGAEGVVENGGIINKIGT
          AAKKRFSVYITESQPDLSGKKMAKALCHLNVPV.VVLDAA.GYIMEKVDLV.VGAEG.VENGG.INK.GT
Retrocopy AAKKRFSVYITESQPDLSGKKMAKALCHLNVPVPVVLDAAAGYIMEKVDLVVVGAEG-VENGGMINKVGT

Parental  NQMAVCAKAQNKPFYVVAESFKFVRLFP-LNQQDVPDKFKYKADTLKSVQAGQDLKEEHPWVDYTA-PSL
          NQMAVCAKAQNKPFYVVAE.F......P.LNQQD.P.KFKYKADTLKSVQAGQDLKEEHPWVDYTA.PSL
Retrocopy NQMAVCAKAQNKPFYVVAE-FQVCTALP>LNQQDAPGKFKYKADTLKSVQAGQDLKEEHPWVDYTA<PSL

Parental  ITLLFTDLGVLTPSAVSDELIKLYL
          ITLLF.DLG.LTPSAVSDELIKL.L
Retrocopy ITLLFRDLGLLTPSAVSDELIKLHL

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	12.08 RPM
SRP014902_testis	0.00 RPM	13.30 RPM
SRP018288_heart	0.03 RPM	7.49 RPM
SRP018288_kidney	0.00 RPM	14.18 RPM
SRP018288_liver	0.00 RPM	7.04 RPM
SRP018288_lung	0.00 RPM	20.06 RPM
SRP018856_adipose	0.21 RPM	42.33 RPM
SRP035408_brain	0.06 RPM	14.23 RPM
SRP035408_liver	0.12 RPM	15.09 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_513 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_513 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007269	1 retrocopy	retro_btau_556,
Sus scrofa	ENSSSCG00000009770	1 retrocopy	retro_sscr_513 ,