RetrogeneDB ID: retro_ptro_2829

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:41584028..41585454(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPJ
• Ensembl ID: ENSPTRG00000015968
• Aliases: None
• Description: recombination signal binding protein for immunoglobulin kappa J region [Source:HGNC Symbol;Acc:5724]

Sequence

>retro_ptro_2829
AAATTTGGTAAGTGGCCTCCACTTAAACGACTTACTAGGGAAGCTATGTGAAATTATTTAAAAGGGTAAGGGGATCAAAT
AGTACTTATCCTTCATGCAAAAGTTGTACAGAAGTCATATGGAAATGAAAAAAGGTTTTTTTGCCCTCCCCCTTGTGTAT
ATCTTATGGGCAGTGGATGGAAGAAAATAAAATAACAAATGAAATGCGATGGTTGTTCTGAACAAGGGTCTCAACCATGT
GCATTTATTGGGATAGGAAATAGTGACCAAGAAATGCAGCAGCTAAACTTGGAAGGAAAGAACTATTGCACAGCCAAAAC
ATTGTACATATCTGATTCAGACAAGCAAAAGCACTTCATGTTGTCTGTAAAGGTGTTCTATGGCAACGGTGATGACATTG
GTGTGTTCCTCAGCAAGTCATCCAAACCTTCCAAAAAGAAGCAGTCATTGAAAAATGCTGACTTATGCATTGCCTCAGGA
ACAAAGGTGGCTCTGTTTAATCGACTACGATCCCAGACAGTTAGTACCAGATACTTGCACGTAGAAAGAGGTAATTTTCA
TGCTAGTTCACAGCAATGGGGAGCATTTTACATTATTCTTGGATGATGATGGATCAGAAGGAGAAGAATTCACAGTCTGA
GATGGCTACATTCATTATGGACAAACAGTCAAACTTGTGTGCTCAGTTACTGGCATGGCACTCCCAAGATTGATAATTAG
GAAAGTTGATAAGCAGACCACATTATTGGATGCAGATGATCCTGTGTCACAACTCCAGAAATGTGCATTTGACCTTGAGG
ATACAGAAAGAAAGTACTTATGCCTTTCTCAAGAAAGAATAATTCAATTTCAGGCCACTCCATGCCCAACAGAACCAAAT
AAAGAGATGATAAATGATGGTGCTTCCTGGGCAATCATTAACACACATAAGGCGAAGTATACATTTTACGAGAGAATGGG
CCCTGTCCTTGCCCTGGTCATGCCTACACCTGTCATAGAGAGCCTTAAGTTGAATGGTGGTGGGGACGAAGCAATGCTTG
AACTTACAGGACAGAATTTCACTCCAAATTTACAAGTGTGGTTTGGGGATGTAGAAGCTGAAGCTATGTACAGGTGTGGA
GAGAGTATGCTCCGTGTTGTCCCAGACGTTTCTGCATTCTGAGAAGGTTGGAGATAGGTCCAGCAACCAGTCCAGGTTTC
AGTAACTTTGGTCCGAAATGATGGAATCATATATTCCACCAGCCTTACCTTTACCTACACACCAGAAGCAGGGCCACGGC
CACATTGCAGTGTAGCAGGCGCAATCCTTCAAGCCAGTTCAAGCCACGTGCCCCCTAATGAATTAAACACAAACAGCGAT
GGAAGTTACACAAATGCCAGCACAAATTCAACCAGTGTCACATCATCTACACCAACAGTGGTATCC

Alignment

ORF - retro_ptro_2829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.07 %
• Parental protein coverage: 96.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKKKKEQMERD
          KFG..PP.KRLTREAM.NYLK..GDQ.VLILHAKV.QKSYGNEKRFFCPPPCVYLMGSGWKK.K.QM..D
Retrocopy KFGKWPPLKRLTREAM*NYLKG*GDQIVLILHAKVVQKSYGNEKRFFCPPPCVYLMGSGWKKIK*QMKCD

Parental  GCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLSKR
          GCSEQ.SQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDK.KHFMLSVK.FYGN.DDIGVFLSK.
Retrocopy GCSEQGSQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKQKHFMLSVKVFYGNGDDIGVFLSKS

Parental  IKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQW-GAFFIHLLDDDE
          ....SKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVE.GNFH..S.Q..G..F...LDDD.
Retrocopy ----SKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVERGNFH-ASSQQ>GEHFTLFLDDDG

Parental  SEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYLC
          SEGEEFTV.DGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQT.LLDADDPVSQL.KCAF.L.DTER.YLC
Retrocopy SEGEEFTV*DGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTTLLDADDPVSQLQKCAFDLEDTERKYLC

Parental  LSQERIIQFQATPCPKEPNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGDVA
          LSQERIIQFQATPCP.EPNKEMINDGASW.II.T.KA.YTFYE.MGPVLA.V.P.PV.ESL.LNGGGD.A
Retrocopy LSQERIIQFQATPCPTEPNKEMINDGASWAIINTHKAKYTFYERMGPVLALVMPTPVIESLKLNGGGDEA

Parental  MLELTGQNFTPNLRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGIIYSTS
          MLELTGQNFTPNL.VWFGDVEAE.MYRCGESML.VVPD.SAF.EGWR.V.QPVQV.VTLVRNDGIIYSTS
Retrocopy MLELTGQNFTPNLQVWFGDVEAEAMYRCGESMLRVVPDVSAF*EGWR*VQQPVQVSVTLVRNDGIIYSTS

Parental  LTFTYTPEPGPRPHCSAAGAILRANSSQVPPNESNTNSEGSYTNASTNSTSVTSSTATVVS
          LTFTYTPE.GPRPHCS.AGAIL.A.SS.VPPNE.NTNS.GSYTNASTNSTSVTSST.TVVS
Retrocopy LTFTYTPEAGPRPHCSVAGAILQASSSHVPPNELNTNSDGSYTNASTNSTSVTSSTPTVVS

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	22.09 RPM
SRP007412_cerebellum	0.00 RPM	32.37 RPM
SRP007412_heart	0.00 RPM	17.02 RPM
SRP007412_kidney	0.03 RPM	20.32 RPM
SRP007412_liver	0.03 RPM	7.73 RPM
SRP007412_testis	0.00 RPM	38.68 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2829 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2829 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003602	1 retrocopy	retro_btau_1507,
Choloepus hoffmanni	ENSCHOG00000001582	4 retrocopies	retro_chof_1172, retro_chof_1278, retro_chof_2449, retro_chof_371,
Homo sapiens	ENSG00000168214	6 retrocopies	retro_hsap_4169, retro_hsap_4171, retro_hsap_4173, retro_hsap_4174, retro_hsap_4256, retro_hsap_4316,
Gorilla gorilla	ENSGGOG00000004582	1 retrocopy	retro_ggor_2853,
Mus musculus	ENSMUSG00000039191	2 retrocopies	retro_mmus_2348, retro_mmus_2819,
Nomascus leucogenys	ENSNLEG00000016895	1 retrocopy	retro_nleu_2305,
Oryctolagus cuniculus	ENSOCUG00000013449	1 retrocopy	retro_ocun_1445,
Pan troglodytes	ENSPTRG00000015968	1 retrocopy	retro_ptro_2829 ,
Tursiops truncatus	ENSTTRG00000009022	2 retrocopies	retro_ttru_1151, retro_ttru_1593,