RetrogeneDB ID: retro_ptro_2175

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:99907979..99909180(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSPTRG00000008963
• Aliases: None
• Description: None

Sequence

>retro_ptro_2175
CTGGGGGAGGCACAGAGGCAGATCAAGGAGTGTGCACCACAGACAAAGGATGTTCTCAAACAGCATTTTAATGATTTAAA
GGGAACCCTTGAGGAGCTCCTGGATGAGTGATTGGTGACCCTTTAGCAAGAGGTGGACATCATTGAGCAGGAGACCATTA
AACCATTAGATGACTGCCAGAGGCTCATAGAACATGGAGTCAACACTGCAGAGGACTTAGTCTGAGTAGGTGAGATTGCC
ATGGTTGGTAGTGTAGAAGAGAATGAGAAACTGTATAGCTTTGCCGAAAAGGTCTCACACATTCAGTTGGACAGCTTACC
AGAAGTACCTTTACTGGTTGATGTGCTTTGTTTATCTGCTCAGTTGGATGACTCAATTCTTATAGTAAAATACTACATTT
CTAAGCATGGAACAGTAGCATCTCTCCCACCAGTACAGATAAAAGAACTGAAACAGAAACCTGGAGTCATCACAGTAGGA
TGGTGTAAGGTGGATGATGATTTTGCAGCCCAAGATTACAGGCTCTAATTTTGTAAACGTACTTCAAATCATTATGAGGA
TGTACATGTAGGTTCTGAAACTCAATTCATAGTACTGCACATGGACTCCAATTTTGATTATCAGTTCGAAGTCTGCACCT
GAGGAGATGGTCAACAGGACTGGAGCCCTGAAGTGTCCCCCAGATAGGTCATTTCACATTGGTGCCTCATGAGTGGACAG
CTGGTTTTGAGGGGTACAGTCTGAAAGTCGAAGTAATATTGCATTCTGGAATGATTCTCAATCCTCAGGTGTTCTCTACT
CTAGAACTCCAACTTATTTCTGTGGGCAGACATTAACATTCAGAGTTGAAACTGTGGGACAGAAGATACAGTATGGGGTG
TTTGCAGAAAAACAGAGTGGATATGACTCTCTGCAGCAGGATCAAGCTATATGTATGAGTACAAATGGTGAAATTTTTGT
TAATGGAAAAGAAATGACTAATGAGTTAACTTCAGTTACTTCTGTGTGCACTGTCACATTTGACATTGAAGCTGTCACTC
TAGGAACCACCAATAATAATGAAGGCAGGAACTTCAAGCTTCGAGTAACAATTAGCTCAAATAACAGAGAAGTGGTTTTT
AATTAGTTACTCGATCAATCTTGTGGTTCTCTTTACTTTGGATGCCCATTTTTCTATCCTGGATGGAAAATATTAGTGTT
T

Alignment

ORF - retro_ptro_2175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.66 %
• Parental protein coverage: 91.86 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LREARRQIKESASQTRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTA
          L.EA.RQIKE.A.QT.DVLKQHFNDLKGTL..LLDE.LVTL.QEVD.IEQETIKPLDDCQ.LIEHGVNTA
Retrocopy LGEAQRQIKECAPQTKDVLKQHFNDLKGTLEELLDE*LVTL*QEVDIIEQETIKPLDDCQRLIEHGVNTA

Parental  EDLVREGEIAMLGGVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGT
          EDLV..GEIAM.G.V.EENEKL.SF..K.SHIQLDSLPEVPLLVDV.CLSAQLDDSIL.IVK..I.KHGT
Retrocopy EDLV*VGEIAMVGSV-EENEKLYSFAEKVSHIQLDSLPEVPLLVDVLCLSAQLDDSIL-IVKYYISKHGT

Parental  VASRPPVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQ
          VAS.PPVQI.EL..KPG.I.V.WCKVDDDF.AQDYRL.F.K.TSNH.EDV.VGSET.FIVLH.D.N.DYQ
Retrocopy VASLPPVQIKELKQKPGVITVGWCKVDDDFAAQDYRL*FCKRTSNHYEDVHVGSETQFIVLHMDSNFDYQ

Parental  FRVCARGDGRQEWSPW-SVPQIGHSTLVPHEWTAGFEGYSLS-SRRNIALRNDSESSGVLYSRAPTYFCG
          F.VC..GDG.Q.WSP..SVPQIGH.TLVPHEWTAGFEGYSL..SR.NIA..NDS.SSGVLYSR.PTYFCG
Retrocopy FEVCT*GDGQQDWSPE<SVPQIGHFTLVPHEWTAGFEGYSLK<SRSNIAFWNDSQSSGVLYSRTPTYFCG

Parental  QTLTFRVETVGQPDRRDSIGVCAEKQDGYDSLQRDQAVCISTNGAVFVNGKEMTNQLPAVTSGSTVTFDI
          QTLTFRVETVGQ.......GV.AEKQ.GYDSLQ.DQA.C.STNG..FVNGKEMTN.L..VTS..TVTFDI
Retrocopy QTLTFRVETVGQ---KIQYGVFAEKQSGYDSLQQDQAICMSTNGEIFVNGKEMTNELTSVTSVCTVTFDI

Parental  EAVTLGTTSNNEGGHFKLRVTISSNNREVVFDWLLDQSCGSLYFGCSFFYPGWKVLVF
          EAVTLGTT.NNEG..FKLRVTISSNNREVVF..LLDQSCGSLYFGC.FFYPGWK.LVF
Retrocopy EAVTLGTTNNNEGRNFKLRVTISSNNREVVFN*LLDQSCGSLYFGCPFFYPGWKILVF

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	0.04 RPM	18.59 RPM
SRP007412_cerebellum	0.00 RPM	25.09 RPM
SRP007412_heart	0.00 RPM	5.33 RPM
SRP007412_kidney	0.00 RPM	6.77 RPM
SRP007412_liver	0.00 RPM	4.62 RPM
SRP007412_testis	0.11 RPM	25.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2175 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2175 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3360
Gorilla gorilla	retro_ggor_2278
Pongo abelii	retro_pabe_2672

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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 ,