RetrogeneDB ID: retro_ggor_2278

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:82980260..82981305(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSGGOG00000005002
• Aliases: None
• Description: None

Sequence

>retro_ggor_2278
CTGGGGGAGGCACAGAGGCAGATCAAGGAGTGTGCACCACAGACAAAGGATGTTCTCAAACAGCATTTTAATGATTTGAA
GGGAACCCTTGAGGAGCTCCTGGATGAGCGATTGGTGACCCTTTAGCAAGAGGTGGACATCATTGAGCAGGAGACCATTA
AACCATTAGATGACTGCCAGAGGCTCATAGAACATGGAGTCAACACTGCAGAGGACTTAGTCTGAGTAGGTGAGATTGCC
ATGGTTGGTAGTGTAGAAGAGGATGAGAAACTGTATAGCTTTGCTGAAAAGGTCTCACACATTCAGTTGGACAGCTTACC
AGAAGTACCTTTACTGGTTGATGTGCTTTGTTTATGTGCTCAGTTGGATGACTCAATTCTTATAGTAAAAGACTACATTT
CTAAGCATGGAACAGTAGCATCTCTCCCACCAATACAGATATAGGAACTGAAACAGAAACCTGGAGTCATCACAGTAGGA
TGGTGTAAGGTGGATGATGATTTTACAGCCCAAGATTACAGGCTCTAATTTTGCAAACGTACTTCAAATCATTATGAGGA
TGTACATGTAGGTTCTGAAACTCAATTCATAGTACTGCACATGGACTCCAATTTTGATTATCAGTTCAAAGTCTGCACCT
GAGGAGATGGTCAACAGGACTGGAGCCCTGAAGTGTCCCCCAGATAGGACATTTCACATTGGTGCCTCATGAGCGGACAG
CTGGTTTTGAGGGGTACAGTCTGAAAGTCGAAGTAATATTGCATTCTGGAATGATTCTCAATCCTCAGGTGTTCTCTACT
CTAGAACTCCAACTTATTTCTGTGGGCAGACATTAACATTCAGAGTTGAAATTGTGGGACAGAAGATACAGTATGGGGTG
TTTGCAGAAAAACAGAATGGATATGACTCTCTGCAGCAGGATCAAGCTACATGTATGAGTACAAATGGTGAAGTTTTTGT
TAATGGAAAAGAAATGACTAATGAGTTAACTTCAGTTACTTCTGTGTGCACTGTCACATTTGACATTGAAGCTGTCACTC
TAGGC

Alignment

ORF - retro_ggor_2278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.93 %
• Parental protein coverage: 80.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LREARRQIKESASQTRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVNTA
          L.EA.RQIKE.A.QT.DVLKQHFNDLKGTL..LLDERLVTL.QEVD.IEQETIKPLDDCQ.LIEHGVNTA
Retrocopy LGEAQRQIKECAPQTKDVLKQHFNDLKGTLEELLDERLVTL*QEVDIIEQETIKPLDDCQRLIEHGVNTA

Parental  EDLVREGEIAMLGGVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGT
          EDLV..GEIAM.G.V.EE.EKL.SF..K.SHIQLDSLPEVPLLVDV.CL.AQLDDSIL.IVKD.I.KHGT
Retrocopy EDLV*VGEIAMVGSV-EEDEKLYSFAEKVSHIQLDSLPEVPLLVDVLCLCAQLDDSIL-IVKDYISKHGT

Parental  VASRPPVQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKCTSNHFEDVYVGSETEFIVLHIDPNVDYQ
          VAS.PP.QI.EL..KPG.I.V.WCKVDDDFTAQDYRL.F.K.TSNH.EDV.VGSET.FIVLH.D.N.DYQ
Retrocopy VASLPPIQI*ELKQKPGVITVGWCKVDDDFTAQDYRL*FCKRTSNHYEDVHVGSETQFIVLHMDSNFDYQ

Parental  FRVCARGDGRQEWSPW-SVPQIGHSTLVPHEKEWTAGFEGYSL-SSRRNIALRNDSESSGVLYSRAPTYF
          F.VC..GDG.Q.WSP..SVPQIGH.TLVPHE...TAGFEGYSL..SR.NIA..NDS.SSGVLYSR.PTYF
Retrocopy FKVCT*GDGQQDWSPE<SVPQIGHFTLVPHER--TAGFEGYSL<ESRSNIAFWNDSQSSGVLYSRTPTYF

Parental  CGQTLTFRVETVGQPDRRDSIGVCAEKQDGYDSLQRDQAVCISTNGAVFVNGKEMTNQLPAVTSGSTVTF
          CGQTLTFRVE.VGQ.......GV.AEKQ.GYDSLQ.DQA.C.STNG.VFVNGKEMTN.L..VTS..TVTF
Retrocopy CGQTLTFRVEIVGQ---KIQYGVFAEKQNGYDSLQQDQATCMSTNGEVFVNGKEMTNELTSVTSVCTVTF

Parental  DIEAVTLG
          DIEAVTLG
Retrocopy DIEAVTLG

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	10.17 RPM
SRP007412_cerebellum	0.00 RPM	17.14 RPM
SRP007412_heart	0.00 RPM	2.13 RPM
SRP007412_kidney	0.00 RPM	7.40 RPM
SRP007412_liver	0.00 RPM	6.20 RPM
SRP007412_testis	0.21 RPM	16.78 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2278 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3360
Pan troglodytes	retro_ptro_2175
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,