RetrogeneDB ID: retro_sscr_878

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:89510315..89510691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2E2
• Ensembl ID: ENSSSCG00000015845
• Aliases: None
• Description: general transcription factor IIE, polypeptide 2, beta 34kDa [Source:HGNC Symbol;Acc:4651]

Sequence

>retro_sscr_878
AAGGCTCTACTTAGTCTCTTAGATAAGCATGACCAGCAAGGCCTAGGAGGAATTCTTTGAGAAGACATAAAGGAAGGACT
CCCCAATTCCCAGAAAGCCATCAAGGCTTTAGGGAACCAGATACTATTTGTAAATCATCCTGATAAGAAGAAAATTCTTT
TCTTCAATGAGAAAAGCTGTCAGTTTTCTGTGAATGAAGAGTTTCAGAAACTGTGGAGGAGTGTCACTGTGGATTCAATG
GATAGGGAGAACACCAAAGAGTATCCAAAGTGACAGGGTATCTCTTCCATGCAGGAATCCGGACCGAAGAAAGTGGCCCC
TATTCAGAGAAGGAAGGAAAAAGCCTTCTCCCCAGAAAAAGCGACGGTTTAAGACT

Alignment

ORF - retro_sscr_878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.03 %
• Parental protein coverage: 60.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KALLRLLDKHDQRGLGGILLEDIEEGLPNSQKAVKALGDQILFVNRPDKKKILFFNDKSCQFSVDEGTEF
          KALL.LLDKHDQ.GLGGIL.EDI.EGLPNSQKA.KALG.QILFVN.PDKKKILFFN.KSCQFSV.E..EF
Retrocopy KALLSLLDKHDQQGLGGIL*EDIKEGLPNSQKAIKALGNQILFVNHPDKKKILFFNEKSCQFSVNE--EF

Parental  QKLWRSVTVDSMDEEKIEEYLKRQGISSMQESGPKKVAPIQRRKKPA-SQKK-RRFKT
          QKLWRSVTVDSMD.E...EY.K.QGISSMQESGPKKVAPIQRRK..A.S..K.RRFKT
Retrocopy QKLWRSVTVDSMDRENTKEYPK*QGISSMQESGPKKVAPIQRRKEKA>SPQKKRRFKT

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	15.13 RPM
SRP014902_testis	0.00 RPM	36.63 RPM
SRP018288_heart	0.00 RPM	40.47 RPM
SRP018288_kidney	0.00 RPM	32.31 RPM
SRP018288_liver	0.32 RPM	17.11 RPM
SRP018288_lung	0.00 RPM	40.93 RPM
SRP018856_adipose	0.00 RPM	55.18 RPM
SRP035408_brain	0.29 RPM	62.00 RPM
SRP035408_liver	0.12 RPM	32.73 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_878 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005031	1 retrocopy	retro_dnov_2321,
Macropus eugenii	ENSMEUG00000010541	1 retrocopy	retro_meug_546,
Myotis lucifugus	ENSMLUG00000007814	1 retrocopy	retro_mluc_2029,
Sorex araneus	ENSSARG00000007758	2 retrocopies	retro_sara_376, retro_sara_569,
Sus scrofa	ENSSSCG00000015845	1 retrocopy	retro_sscr_878 ,
Tarsius syrichta	ENSTSYG00000013143	1 retrocopy	retro_tsyr_2074,
Tursiops truncatus	ENSTTRG00000012464	1 retrocopy	retro_ttru_859,