RetrogeneDB ID: retro_pabe_2672

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:100132391..100133589(+)
• 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_2672
CTGTGGGAGGCACAGAGGCAGATCAAGGAGTGTGCACCACAGACAAAGGATGTTCTTAAACAGCATTTTAATGATTTAAA
GGGAACCCTTGAGGAGCTCCTGGATGAGCGATTGGTGACCCTTTAGCAAGAGGTGGACATCGTTGAGCAGGAGACCATTA
AACCATTAGATGACTGCCAGAGGCTCATAGAACACGGAGTCAACACTGCAGAGGACTTAGTCTGAGTAGGTGAGATTGCC
ATGGTTGGTAGTGTAGAAGAGAATGAGCAACAGTATAGCTTTACCAAAAAGGTCTCACACATTCAGTTGGACAGCTTACC
AGAAGTACCTTTACTGGTTGATGTGCTTTGTTTATCTGCTCAGTTGGATGACTCAATTCTTATAGTAAAAGACTACATTT
CTAAGCATGGAACAGTAGCATCTCTCCCACCAGTACAGATATAAGAACTGATACAGAAACCTGGAGTCATCACAGTAGGA
TGGTGTAAGGTGGATGATGATTTTACAGCCCAAGATTATAGGCTCTAATTTTGTAAATGTACTTCAAATCATTATGAGGA
TGTACATGTAGGTTCTGAAACTCAATTCATAGTACTGCACATGGACTCCAATGTTGATTATCAGTTCAATGTCTGCACCT
GAGGAGATGGTCAACAGGAGTGCAGCCCCGAAGTGTCCCCCAGATAGGTCATTTCACATTGATGCCTCATGAGTGGACAG
CTGGTTTTGAGGGGTACAGTCTGAAAGTCGAAGTAATATTGCATTCTGGAATGATTCTCAATCCTCAGGTGTTCTCTACT
CTAGAACTCCAACTTATTTCTGTGGGCAGACATTAACATTCAGAGTTGAAATTGTGGGACAGAAGAGACAGTACGGGGTG
TTTGCAGAAAGACGGAATGGATATGACTCTCTGCAGCAGGATCAAGCTATATGTATGAGTACAAACGGTGAAGTTTTTGT
TAATGGAAAAGAAATGACTAATGAGTTAACTTCAGTTACTTCTGGGTGCACTGTCACATTTGACATTGAAGCTGTCACTC
TAGGAACCACCAATAATAATGAAGGCAGGAACTTCAAGCTTCGAGTAACAATTAGCTCAAATAACAGAGAAGTGGTTTTT
AATTAGTTACTCGATCAATCTTGTGGTTCTCTTTACTTTGGATGCTCATTTTTCCATCCTGGATGGAAAATATTAGTG

Alignment

ORF - retro_pabe_2672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.34 %
• Parental protein coverage: 91.63 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LREARRQIKESASQTRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTA
          L.EA.RQIKE.A.QT.DVLKQHFNDLKGTL..LLDERLVTL.QEVD..EQETIKPLDDCQ.LIEHGVNTA
Retrocopy LWEAQRQIKECAPQTKDVLKQHFNDLKGTLEELLDERLVTL*QEVDIVEQETIKPLDDCQRLIEHGVNTA

Parental  EDLVREGEIAMLGGVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGT
          EDLV..GEIAM.G.V.EENE...SFTKK.SHIQLDSLPEVPLLVDV.CLSAQLDDSIL.IVKD.I.KHGT
Retrocopy EDLV*VGEIAMVGSV-EENEQQYSFTKKVSHIQLDSLPEVPLLVDVLCLSAQLDDSIL-IVKDYISKHGT

Parental  VASRPPVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQ
          VAS.PPVQI.ELI.KPG.I.V.WCKVDDDFTAQDYRL.F.KCTSNH.EDV.VGSET.FIVLH.D.NVDYQ
Retrocopy VASLPPVQI*ELIQKPGVITVGWCKVDDDFTAQDYRL*FCKCTSNHYEDVHVGSETQFIVLHMDSNVDYQ

Parental  FRVCARGDGRQEWS-PWSVPQIGHSTLVPHEWTAGFEGYSL-SSRRNIALRNDSESSGVLYSRAPTYFCG
          F.VC..GDG.QE.S.P.SVPQIGH.TL.PHEWTAGFEGYSL..SR.NIA..NDS.SSGVLYSR.PTYFCG
Retrocopy FNVCT*GDGQQECS<PRSVPQIGHFTLMPHEWTAGFEGYSL<ESRSNIAFWNDSQSSGVLYSRTPTYFCG

Parental  QTLTFRVETVGQPDRRDSIGVCAEKQDGYDSLQRDQAVCISTNGAVFVNGKEMTNQLPAVTSGSTVTFDI
          QTLTFRVE.VGQ.......GV.AE...GYDSLQ.DQA.C.STNG.VFVNGKEMTN.L..VTSG.TVTFDI
Retrocopy QTLTFRVEIVGQ---KRQYGVFAERRNGYDSLQQDQAICMSTNGEVFVNGKEMTNELTSVTSGCTVTFDI

Parental  EAVTLGTTSNNEGGHFKLRVTISSNNREVVFDWLLDQSCGSLYFGCSFFYPGWKVLV
          EAVTLGTT.NNEG..FKLRVTISSNNREVVF..LLDQSCGSLYFGCSFF.PGWK.LV
Retrocopy EAVTLGTTNNNEGRNFKLRVTISSNNREVVFN*LLDQSCGSLYFGCSFFHPGWKILV

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_2672 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2672 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3360
Pan troglodytes	retro_ptro_2175
Gorilla gorilla	retro_ggor_2278

---

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,