RetrogeneDB ID: retro_sscr_154

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:47687695..47688745(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000004243
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPD1L
• Ensembl ID: ENSSSCG00000021977
• Aliases: None
• Description: glycerol-3-phosphate dehydrogenase 1-like [Source:HGNC Symbol;Acc:28956]

Sequence

>retro_sscr_154
GCCACGGCCCCCCTGAAAGTGTGCATCGTGGGCTCAGGCAACTGGGGTTCAGCTATTGCAAAAATAATTGGTGATAATGT
AAAAAAACTACAGAAATTTGTCTCCTTGGTCAAGATGTGGGTCTTTGAAGAAATAGTTAATGGGAGAAAACTGACAGACA
TCATAAATAATGACCATGAAAATGTAAAATATCTCCCTGGATACAAGCTCCCAGAAAATGTAGTTGCGGTCTCCAGCCTC
AGGGAGGCAGTGAAGGACGCAGACCTGCTGGTGTTTGTTATCCCACACCAGTTCATTCACGCGATCTGCGATGAGATCAT
TGGGAAAGTGCACAAGGACGCAGTGGGCATCACACTCATCAAGGGCGTAGACGAGGGTCCCCAGGGGCTGAGGCTTATTT
CCGAGGTCATCCGAGAGAAGCTAGGCATTGACATCAGTGTGCTGATGGGAGCCAACACAGCCAATGAGGTGGCTGCTGGA
AAGTTCTGTGAGACCACCATCGGCAGCAAGATACTAGAGAATGGCCTTCTTTTCAAAGAACTTCTGGAGACTCCGAATTT
CCGAATTACGGTGGTTGATGATGCAGACACTGTTGAAATTTGTGGTGCCCTGAAGAACATCGTGGCCGTGGGAGCCGGGT
TCTGCGATGGCCTCCACTATGGCAACAACACCAAGGCTGCCGCCATCCGACTGGGGCTCATGGAAATGATCGCCTTCGCC
AGGATCTTCTGCACGGGCCAGGTGTCCACGAACACCTTCCTGGAGAGCTGCGGCGTGGCGGACCTGATCACCACCTGCTA
TGCAGGCCGGAACCGCAAGGTGGCGGAAGCTTTTGCCAGGACCGGAAAGACCCTTGAAGAACTGGAGAAGGAGATGCTGA
ATGGGCAGAAGCTGCAAGGTCCTCAGACTTCCGCTGAGGTGTACCGCGTCCTCAAACAGAGGGGGCTGCTCAACAAGTTT
CCACTGTTCACTGCGGTGTACCAGATCTGCTACGAAGGCAGGCCTGTTGAAGAGATGTTGTCTTGTCTCCAGAGCCATCC
AGAGCATATA

Alignment

ORF - retro_sscr_154 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.29 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASPLKVCIVGSGNWGSAVAKIIGDNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHKL
          A..PLKVCIVGSGNWGSA.AKIIGDNVKKLQKF.S.VKMWVFEE.VNGRKLTDIINNDHENVKYLPG.KL
Retrocopy ATAPLKVCIVGSGNWGSAIAKIIGDNVKKLQKFVSLVKMWVFEEIVNGRKLTDIINNDHENVKYLPGYKL

Parental  PENVVAVANLGEAVKDADLLVFVIPHQFIHRICDEITGRVPKDALGITLIKGIDEGPEGLKLISDIIREK
          PENVVAV..L.EAVKDADLLVFVIPHQFIH.ICDEI.G.V.KDA.GITLIKG.DEGP.GL.LIS..IREK
Retrocopy PENVVAVSSLREAVKDADLLVFVIPHQFIHAICDEIIGKVHKDAVGITLIKGVDEGPQGLRLISEVIREK

Parental  MGIDISVLMGANIANEVAAGKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNIVAV
          .GIDISVLMGAN.ANEVAAGKFCETTIGSK..ENGLLFKELL.TPNFRITVVDDADTVE.CGALKNIVAV
Retrocopy LGIDISVLMGANTANEVAAGKFCETTIGSKILENGLLFKELLETPNFRITVVDDADTVEICGALKNIVAV

Parental  GAGFCDGLRCGDNTKAAVIRLGLMEMIAFARIFCKGQVSTATFLESCGVADLITTCYGGRNRRVAEAFAR
          GAGFCDGL..G.NTKAA.IRLGLMEMIAFARIFC.GQVST.TFLESCGVADLITTCY.GRNR.VAEAFAR
Retrocopy GAGFCDGLHYGNNTKAAAIRLGLMEMIAFARIFCTGQVSTNTFLESCGVADLITTCYAGRNRKVAEAFAR

Parental  TGKTIEELEKEMLNGQKLQGPQTAAEVYRILKQKGLVDKFPLFTAVYQICYEGRPVQEMLSCLQSHPEHI
          TGKT.EELEKEMLNGQKLQGPQT.AEVYR.LKQ.GL..KFPLFTAVYQICYEGRPV.EMLSCLQSHPEHI
Retrocopy TGKTLEELEKEMLNGQKLQGPQTSAEVYRVLKQRGLLNKFPLFTAVYQICYEGRPVEEMLSCLQSHPEHI

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	13.41 RPM
SRP014902_testis	0.00 RPM	30.84 RPM
SRP018288_heart	0.00 RPM	385.20 RPM
SRP018288_kidney	0.00 RPM	157.41 RPM
SRP018288_liver	0.00 RPM	79.16 RPM
SRP018288_lung	0.00 RPM	78.92 RPM
SRP018856_adipose	0.00 RPM	49.15 RPM
SRP035408_brain	0.00 RPM	12.77 RPM
SRP035408_liver	0.00 RPM	40.39 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_154 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_154 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1671

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348, retro_mmus_2552, retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529, retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035, retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154 ,