RetrogeneDB ID: retro_sscr_810

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:25136746..25137235(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TYMS
• Ensembl ID: ENSSSCG00000023869
• Aliases: None
• Description: thymidylate synthetase [Source:HGNC Symbol;Acc:12441]

Sequence

>retro_sscr_810
TTTTCAGGTGGAAAAGTGGACCAACTGCAAAAGGTGATTGACACAATCGTAAGCAACACTGACAACACAACAATCATCCT
GTGTGCTTGGAATCCAAAAGATCTTCTTGTGGCCCTCTCCCACTCTGCTGCCTGTGCCTCGCCCTTTGCCAGTTCTGTGT
AGTGAACTGTGAGCTGCCCTGCCAGCTATATCAGAGGTCGGGAGATGGTCCTGGGTGTGCCCTTCAACATCAGCAGCTAC
CTCCCTGCTCACCTACACGATCACACACGTTACAGGTCTGAAGCTGGGCGACTTTGTACACGCTTTGGGATATGCACACG
TCTATCTGAACCACACTGAGCCGCTGAAAATGAAGCTTCAGGGAGAACCAAGGCCTTTCCTAGAGCTCTAAATACTTGGA
AAAGTTGAGAACATGAGTGATATAAGACTGAAGACTTTCAGATTGAAGGCTACAGTCCTCATATGACTATTGAAATGGAA
ATGGCTGTT

Alignment

ORF - retro_sscr_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.64 %
• Parental protein coverage: 98.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YSGQGVDQLQKVIDTIKTNPDDRRIILCAWNPKDLPLMALP-PCHALC----QFYVVNGELSCQLYQRSG
          .SG..VDQLQKVIDTI..N.D...IILCAWNPKDL.L.AL..P...LC....QF.VVN.EL.CQLYQRSG
Retrocopy FSGGKVDQLQKVIDTIVSNTDNTTIILCAWNPKDL-LVALS<PLCCLCLALCQFCVVNCELPCQLYQRSG

Parental  DMGLG-VPFNIASY-ALLTYMIAHITGLKPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPFPKLKILRKV
          D.G.G.VPFNI.SY..LLTY.I.H.TGLK.GDFVH.LG.AH.YLNH.EPLK..LQ.EPRPF..L.IL.KV
Retrocopy D-GPG>VPFNISSY>SLLTYTITHVTGLKLGDFVHALGYAHVYLNHTEPLKMKLQGEPRPFLEL*ILGKV

Parental  EKIDD-FKAEDFQIEGYNPHPTIKMEMAV
          E...D..K.EDFQIEGY.PH.TI.MEMAV
Retrocopy ENMSD<YKTEDFQIEGYSPHMTIEMEMAV

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	1.46 RPM
SRP014902_testis	0.00 RPM	9.48 RPM
SRP018288_heart	0.00 RPM	1.07 RPM
SRP018288_kidney	0.00 RPM	0.99 RPM
SRP018288_liver	0.00 RPM	1.92 RPM
SRP018288_lung	0.00 RPM	2.95 RPM
SRP018856_adipose	0.00 RPM	0.68 RPM
SRP035408_brain	0.00 RPM	0.25 RPM
SRP035408_liver	0.00 RPM	2.67 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_810 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_810 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000014910	2 retrocopies	retro_lafr_1030, retro_lafr_635,
Macropus eugenii	ENSMEUG00000009507	1 retrocopy	retro_meug_175,
Monodelphis domestica	ENSMODG00000021479	2 retrocopies	retro_mdom_1084, retro_mdom_1186,
Mus musculus	ENSMUSG00000025747	1 retrocopy	retro_mmus_584,
Otolemur garnettii	ENSOGAG00000024349	2 retrocopies	retro_ogar_2956, retro_ogar_3211,
Sarcophilus harrisii	ENSSHAG00000003102	1 retrocopy	retro_shar_424,
Sus scrofa	ENSSSCG00000023869	2 retrocopies	retro_sscr_810 , retro_sscr_841,