RetrogeneDB ID: retro_sscr_1203

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:74377924..74378716(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000031063
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUCB2
• Ensembl ID: ENSSSCG00000013380
• Aliases: None
• Description: nucleobindin 2 [Source:HGNC Symbol;Acc:8044]

Sequence

>retro_sscr_1203
CTTTCAGATACAGGCATAGACCACCATGCTCTTCTAAAACAATTCAATCACCTAAACAACCTGAATCCTGACAAGTTTGA
ATCTACAGATTTAGATATGATAATCAAAGTGGCTACAAGTGGTATGGAACACTATGACAAGGCTCGACATGAAGAGTTTA
AAAAATATGAAATGATGAAGGAACATGAAAGGAGAGAATATTTAAAAACACTGACTGAAGAAAAGAGAAAAGAAGAAGAA
TCAAAATTTGAAGAAATGAAGAAAAAGCATGGAAATCATCCCAAAGTTAATCATCCAGGAAGCAAAGATCAACTAAAAGA
AGTGTGGGAAGAGACTGATGGATTGGATCCTAATGACTTTGACCCCAAGACATTTTTCAAATTACATGATGTCAATGGTG
ATGGCTTCCTAGATTAACAAGAATTAGAAGCCCTGTTTCCTAAAGAGTTGGAGAAAGTATATAACCCCAGAAATGAAGAG
GATGACATGGTAGAAATGGAGGAAGAGAGGCTTAGAATGAGGGAACATGTCATGAATGAGGTTGATACTAACAAAGACTG
ATTAGTGACTCTAGAAGAGTTTTTGAAAGCTGCAGAAAAAAAGGAATTCTTGGAGCCAGATAGCTGGGAGACACTGGATC
AGCAACAGTTCTTCACAGAAGAAGAACTGAAAGAATATGAAAATCTTATCTCTGTACAAGAAACTGAACTTAAGAAAAAG
GCAGATGAGCTTCGGAAACAAAAAGAAGAGCTACAACATCAGCATGACCAACTAGAGGCTCAGGTTGTGCAG

Alignment

ORF - retro_sscr_1203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.36 %
• Parental protein coverage: 63.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQDTGIDHHALLKQFDHLNHLNPDKFESTDLDMLIKAATSDLEHYDKARHEEFKKYEMMKEHERREYLKT
          L.DTGIDHHALLKQF.HLN.LNPDKFESTDLDM.IK.ATS..EHYDKARHEEFKKYEMMKEHERREYLKT
Retrocopy LSDTGIDHHALLKQFNHLNNLNPDKFESTDLDMIIKVATSGMEHYDKARHEEFKKYEMMKEHERREYLKT

Parental  LTEEKRKEEESKFEEMKKKHGNHPKVNHPGSKDQLKEVWEETDGLDPNDFDPKTFFKLHDVNGDGFLDEQ
          LT.................HGNHPKVNHPGSKDQLKEVWEETDGLDPNDFDPKTFFKLHDVNGDGFLD.Q
Retrocopy LTXXXXXXXXXXXXXXXXXHGNHPKVNHPGSKDQLKEVWEETDGLDPNDFDPKTFFKLHDVNGDGFLD*Q

Parental  ELEALFTKELEKVYDPKNEEDDMVEMEEERLRMREHVMNEVDTNKDRLVTLEEFLKATEKREFLEPDSWE
          ELEALF.KELEKVY.P.NEEDDMVEMEEERLRMREHVMNEVDTNKD.LVTLEEFLKA.EK.EFLEPDSWE
Retrocopy ELEALFPKELEKVYNPRNEEDDMVEMEEERLRMREHVMNEVDTNKD*LVTLEEFLKAAEKKEFLEPDSWE

Parental  TLDQQQFFTEEELKEYENLISVQETELKKKADELQKQKEELQRQHDQLEAQKLE
          TLDQQQFFTEEELKEYENLISVQETELKKKADEL.KQKEELQ.QHDQLEAQ...
Retrocopy TLDQQQFFTEEELKEYENLISVQETELKKKADELRKQKEELQHQHDQLEAQVVQ

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	9.69 RPM
SRP014902_testis	0.28 RPM	17.12 RPM
SRP018288_heart	0.05 RPM	13.67 RPM
SRP018288_kidney	0.10 RPM	6.30 RPM
SRP018288_liver	0.16 RPM	33.90 RPM
SRP018288_lung	0.20 RPM	21.18 RPM
SRP018856_adipose	0.00 RPM	7.71 RPM
SRP035408_brain	0.19 RPM	104.81 RPM
SRP035408_liver	0.47 RPM	299.46 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1203 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1203 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sus scrofa	ENSSSCG00000013380	1 retrocopy	retro_sscr_1203 ,