RetrogeneDB ID: retro_pabe_1925

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:11228459..11229187(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSPPYG00000008142
• Aliases: None
• Description: cytokine receptor-like factor 3 [Source:HGNC Symbol;Acc:17177]

Sequence

>retro_pabe_1925
TGCCAGAAGCTCATAGAACACCAGAGTCAACACTCCAGAGGGCTTAGTCCGAGAAGGTGAGATTGCCATGCTTGGTGGTG
TAGGAGAAGAGAATGAGAAACTGTGTGAGCTTTACCAAAAAGGCCTTGCACGTTCAGTTGGACAGAATACCAGAAGTACC
TTTACTGGTTGATGTGCCTTGTTTATCTTCTCAGTTGGATGAGTCTATTCTTAACCTCATGAAAGACCACATTCTTAAGC
ATGGAACAGTAGCATCTCGCCCACCAATACAGATAGGAGAACTGATAGAGAAACCTGGAGGCATCATAGTACAATGGTGT
AAGGTGGATGATGACTGTACGGCACAAGATGACAGCCTCCAGTTTCGTAAATGTATTTCAAATCATTTTGAGGATGTATA
TGTAGGTTCTGAAACTGAATTCATAGTATTGCACACAGAATCCAACGTTGAAGATCATTTCAGAATCTGCACCCAAAGAG
ATGGCTGACAGGAGCGGAGTCCTTGGAGTGTCCCCCAGATAGTTCATTCCACATTGGATCCTCATGAGTGGACAGCTGGT
TTTAAGGGGAACAGTCTGAGCAATTGAAGAAATATGTCGTGCTGAAACGATTCTGAATCTTCAGGTGTTCTTGACTCCGG
AGCTTCAACTTATTTCTCTGGGCAGACATTAATATTTAGAGTTGAAACTGTGGGACTACCAGACAGAAGAGACAGTATAG
GAGTGTGT

Alignment

ORF - retro_pabe_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.51 %
• Parental protein coverage: 54.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CQKLIEHG-VNTAEDLVREGEIAMLGGVGEENEKLW-SFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDS
          CQKLIEH..VNT.E.LVREGEIAMLGGVGEENEKL..SFTKKA.H.QLD..PEVPLLVDVPCLS.QLD.S
Retrocopy CQKLIEHQ>VNTPEGLVREGEIAMLGGVGEENEKLC>SFTKKALHVQLDRIPEVPLLVDVPCLSSQLDES

Parental  ILNIVKDHIFKHGTVASRPPVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSET
          ILN..KDHI.KHGTVASRPP.QI.ELIEKPGGIIV.WCKVDDD.TAQD..LQFRKC.SNHFEDVYVGSET
Retrocopy ILNLMKDHILKHGTVASRPPIQIGELIEKPGGIIVQWCKVDDDCTAQDDSLQFRKCISNHFEDVYVGSET

Parental  EFIVLHIDPNVDYQFRVCARGDGRQEWSPWSVPQIGHSTLVPHEWTAGFEGYSLSSRRNIALRNDSESSG
          EFIVLH...NV...FR.C...DG.QE.SPWSVPQI.HSTL.PHEWTAGF.G.SLS..RN....NDSESSG
Retrocopy EFIVLHTESNVEDHFRICTQRDG*QERSPWSVPQIVHSTLDPHEWTAGFKGNSLSN*RNMSC*NDSESSG

Parental  VLYSRAPTYFCGQTLTFRVETVGQPDRRDSIGVC
          VL.S.A.TYF.GQTL.FRVETVG.PDRRDSIGVC
Retrocopy VLDSGASTYFSGQTLIFRVETVGLPDRRDSIGVC

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.55 RPM
SRP007412_cerebellum	0.00 RPM	17.75 RPM
SRP007412_heart	0.00 RPM	4.61 RPM
SRP007412_kidney	0.00 RPM	5.70 RPM
SRP007412_liver	0.00 RPM	5.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1925 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1925 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2133
Pan troglodytes	retro_ptro_1560
Gorilla gorilla	retro_ggor_1649
Macaca mulatta	retro_mmul_1002

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014163	1 retrocopy	retro_cjac_1183,
Homo sapiens	ENSG00000176390	3 retrocopies	retro_hsap_2121, retro_hsap_2133, retro_hsap_3360,
Gorilla gorilla	ENSGGOG00000005002	3 retrocopies	retro_ggor_1644, retro_ggor_1649, retro_ggor_2278,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Mus musculus	ENSMUSG00000017561	1 retrocopy	retro_mmus_368,
Nomascus leucogenys	ENSNLEG00000005850	4 retrocopies	retro_nleu_1957, retro_nleu_2534, retro_nleu_2899, retro_nleu_2900,
Pongo abelii	ENSPPYG00000008142	3 retrocopies	retro_pabe_1925 , retro_pabe_1984, retro_pabe_2672,
Pan troglodytes	ENSPTRG00000008963	2 retrocopies	retro_ptro_1560, retro_ptro_2175,