RetrogeneDB ID: retro_ptro_1281

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:8192976..8194534(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFWD2
• Ensembl ID: ENSPTRG00000001711
• Aliases: None
• Description: None

Sequence

>retro_ptro_1281
ATGTCTGGTAGCCACCATGCCGGGTCAGACTCCACTGGGACGAGCCCCTGCTCCTCAGCCTCTTTGGTGACTTTTGCCTC
CTTGTCCTTATCATCTTCCCCATTGCCGCCACTGTGGCAGCTTCGGCAGTGGTGCTGCTGTCCAGTGGGGTGGCCCAGGC
CACCAGCTTGGATAGCCTTGGGGCCCAGTGTGGCCTGTGTTGGTGGTGCCCACTGTGTCAGGCAGTGGCAAGGTGCTGTC
CATAGTCCTGTCCCAGCTCAGCTGCAGGCCCAGGCCCCAGTGCTGGTATAGGAGGCAGCAGCTGTAGCCTAGGCAGCAGC
AGGAAGCAACCTCTGCTTGCCCCTCCCCTCTCCAACAGGCTCGTCAACTCATATAAGGACAACAGCAATGATTTCATATG
CCCCATCTGCTTTGATATGATTGAAGAGGCATACACGACAAAATAAGGCCACAGCTTTTGCTATAAGTAGATTCACTAGA
GTTCGGAGGATAATAATATATGTACCAAGTATAACTATGTTGTGGACAATACTAACCATCTGTTTCCTAATTTGTTGGTG
AATGAGCTCATTCTCAAACAGAAGCAAAGATTTGAGGAAAAGAGGTTCAAATTGGACCACTCAGTGAGCAGCACCAATGG
CCACAGGTGGCGAATATTTCAAGATTTGTTGGGAACTGACCAAGATAACCTTGATTTGGCCAATATCAACCTCATGTTGG
AGTTACTAGTTCAGAAGAAGAAACAACTGGAAGCAGAATCACATGCAGCCCAACTACAGAATCTTATACAATTCCTCAAG
GTTGCAAGAAGAAATAGGAGAGAGCAACTGGGACAGTTCCAGAAGGAGCTAAGTGTTTTGGAAGAGGATATTAAAAGAGT
GGAAGAAATGAGTGGCTTACACTCTCCTGTCAGTGAGGATAGCACAGTGCCTCAACTTGAAGCTCCTCCTGCATCACACA
GTAGCATTATGGATTCCACAGAATATAGCCAACATCCAGGTTTCAGTGGCAGTTCTTAGACAAAGAAACAGCCTTGATAT
AACAGCACATTAACATCAAAATTAAAATGGCCCACTGCTCATTTTGAAGACCTGGAGCACTGTTACTTTTCTACAAGGTT
GTCTCATATCTCAGATGACAGTTGAACTGCAAGCCAATTGGATGAACTTCAGAAATGCTTGTCCAAGGTTACTCAATATA
AATCAATATGAACTTTAGCCACATTATCATGCCCTAGTGATCTCTATAATGATTCCAGGATAGTCTCTGGTATTGAATTT
GACCAGGATTGTGACTATTTTGCAATTGCTGAGGTTACAATGAAGATTAACGTCTATGAATATGGCACAGTCATCCAGGA
TGGAGTGGATATTCATTACCGTGTGAATGAAATGACCTCAATTCCAAAATCAGCTGTATCAGTTGGAGTAGTTACCATAA
GAACCTGTTAGCTAGCAGTGATTATGAAGGCATTGTTATCCTATGGGATGGATTCACAGGACAGAGGTCAAAGGTCTAAC
AGGAGCATGAGAAGAGGTGTTGAAGTGTTTCATTTGAT

Alignment

ORF - retro_ptro_1281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.37 %
• Parental protein coverage: 71.41 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPP-SVAVSAAALVSGGVAQAAGSGGLG-GPVRPV
          MSGS..AGS.S.GTSP.SSA.S.VT.AS.SLSSSP.PP..VA.SA..L.S.GVAQA.....LG.GPV.PV
Retrocopy MSGSHHAGSDSTGTSPCSSA-SLVTFASLSLSSSPLPP<TVAASAVVLLSSGVAQATSLDSLG<GPVWPV

Parental  LVAPAVSGSGGGAVSTGLSRHSCAARP-SAGVGGSSSSLGSGSRKRPLLAP-LCNGLINSYEDKSNDFVC
          LV.P.VSGSG....S..LS..SC..RP.SAG.GGSS.SLGS.SRK.PLLAP.L.N.L.NSY.D.SNDF.C
Retrocopy LVVPTVSGSGK-VLSIVLSQLSCRPRP>SAGIGGSSCSLGS-SRKQPLLAPPLSNRLVNSYKDNSNDFIC

Parental  PICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNIDHLYPNFLVNELILKQKQRFEEKRFK
          PICFDMIEEAY.TK.GHSFCYK.IH.S.EDNN.C.K.NYVVDN..HL.PN.LVNELILKQKQRFEEKRFK
Retrocopy PICFDMIEEAYTTK*GHSFCYK*IH*SSEDNNICTKYNYVVDNTNHLFPNLLVNELILKQKQRFEEKRFK

Parental  LDHSVSSTNGHRWQIFQDWLGTDQDNLDLANVNLMLELLVQKKKQLEAESHAAQLQILMEFLKVARRNKR
          LDHSVSSTNGHRW.IFQD.LGTDQDNLDLAN.NLMLELLVQKKKQLEAESHAAQLQ.L..FLKVARRN.R
Retrocopy LDHSVSSTNGHRWRIFQDLLGTDQDNLDLANINLMLELLVQKKKQLEAESHAAQLQNLIQFLKVARRNRR

Parental  EQLEQIQKELSVLEEDIKRVEEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQ
          EQL.Q.QKELSVLEEDIKRVEEMSGL.SPVSEDSTVPQ.EAP..SHSSI.DSTEYSQ.PGFSGSS.TKKQ
Retrocopy EQLGQFQKELSVLEEDIKRVEEMSGLHSPVSEDSTVPQLEAPPASHSSIMDSTEYSQHPGFSGSS*TKKQ

Parental  PWYNSTLASRRKRLTAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASD
          P.YNSTL.S..K..TAHFEDLE.CYFSTR.S.ISDDS.TASQLDE.Q.CLSK.T.Y.S...LATLS..SD
Retrocopy P*YNSTLTSKLKWPTAHFEDLEHCYFSTRLSHISDDS*TASQLDELQKCLSKVTQYKSI*TLATLSCPSD

Parental  LYNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMT-CNSKISCISWSSYHKNL
          LYN.S.IVS.IEFD.DCDYFAIA.VT.KI.VYEY.TVIQD.VDIHY..NEMT..NSKISCISWSSYHKNL
Retrocopy LYNDSRIVSGIEFDQDCDYFAIAEVTMKINVYEYGTVIQDGVDIHYRVNEMT<LNSKISCISWSSYHKNL

Parental  LASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFN
          LASSDYEG.VILWDGFTGQRSKV.QEHEKRC.SV.F.
Retrocopy LASSDYEGIVILWDGFTGQRSKV*QEHEKRC*SVSFD

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	14.44 RPM
SRP007412_cerebellum	0.07 RPM	13.01 RPM
SRP007412_heart	0.03 RPM	8.25 RPM
SRP007412_kidney	0.00 RPM	16.48 RPM
SRP007412_liver	0.00 RPM	12.37 RPM
SRP007412_testis	0.00 RPM	36.15 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1281 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1281 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1366
Macaca mulatta	retro_mmul_1342

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000013437	1 retrocopy	retro_ggor_1366,
Macaca mulatta	ENSMMUG00000002072	1 retrocopy	retro_mmul_1342,
Mus musculus	ENSMUSG00000040782	1 retrocopy	retro_mmus_3678,
Nomascus leucogenys	ENSNLEG00000015420	1 retrocopy	retro_nleu_1225,
Pan troglodytes	ENSPTRG00000001711	1 retrocopy	retro_ptro_1281 ,
Pan troglodytes	ENSPTRG00000021702	5 retrocopies	retro_ptro_1802, retro_ptro_1909, retro_ptro_2226, retro_ptro_2987, retro_ptro_896,