RetrogeneDB ID: retro_ggor_2853

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:41612772..41614216(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPJ
• Ensembl ID: ENSGGOG00000004582
• Aliases: None
• Description: None

Sequence

>retro_ggor_2853
ATGGCATGGATTAAAAGGAAATTTGGTAAGTGGTCTCCATTTAAACGACTTACTAGGGAAGCTATGTGAAATTATTTAAA
AGGGTAAGGGGATCAAATAGTACTTACCCTTCATGCAAAAGTTGTACAGAAGTCATATGGAAATGAAAAAAGGTTTTTTT
GCCCTCCCCCTTGTGTATATCTTATGGGCAGTGGATGGAAGAAAATAAAATAACAAATGAAATGCGATGGTTGTTCTGAA
CAAGGGTCTCAACCATGTGCATTTATTGGGATAGGAAATAGTGACCAAGAAATGCAGCAGCTAAACTTGGAAGGAAAGAA
CTATTGCACAGCCAAAACATTGTACATATCTGATTTAGACAAGCAAAAGCACTTCATGTTGTCTGTAAAGGTGTTCTATG
GCAACGGTGATGACATTGGTGTGTTCCTCAGCAAGTCGTCCAAACCTTCCAAAAAGAAGCAGTCATTGAAAAATGCTGAC
TTATGCATTGCCTCAGGAACAAAGGTGGCTCTGTTTAATCGACTACTATCCCAGACAGTTAGTACCAGATACTTGCACGT
AGAAAGAGGTAATTTTCATGCTAGTTCACAGCAATGGGGAGCATTTTACATTATTCTTGGATGATGATGGATCAGAAGGA
GAAGAATTCACAGTCTGAGATGGCTACATTCATTATGGACAAACAGTCAAACTTGTGTGCTCAGTTACTGGCATGGCACT
CCCAAGATTGATAATTAGGAAAGTTGATAAGCAGACCACATTATTGGATGCAGATGATCCTGTGTCACAACTCCATAAAT
GTGCATTTGACCTTGAGGATACAGAAAGAAAGTACTTATGCCTTTCTCAAGAAAGAATAATTCAATTTCAGGCCACTCCA
TGCCCAACAGAACCAAATAAAAAGATGATAAATGATGGTGCTTCCTGGGCAATCATTAGCACACATAAGGGGAAGTATAC
ATTTTACGAGAGAATGGGCCCTGTCCTTGCCCTGGTCATGCCTACGCCTGTCGTAGAGAGCCTTAAGTCGAATGGCGGTG
GGGACGAAGCAATGCTTGAACTTACAGGACAGAATTTCACTCCAAATTTGCAAGTGTGGTTTGGGGATGTAGAAGCTGAA
GCTATGTACAGGTGTGGAGAGAGTATGCTCCGTGTTGTCCCAGACGTTTCTGCATTCTGAGAAGGTTGGAGATAGGTCCA
GCAACCAGTCCAGGTTTCAGTAACTTTGGTCCGAAATGATGGAATCATATATTCCACCAGCCTTACCTTTACCTACACAC
CAGAAGCAGGGCCGCGGCCACATTGCAGTGTAGCAGGCGCAATCCTTCAAGCCAGTTCAAGCCACGTGCCCCCTAATGAA
TTAAACACAAACAGCGATGGAATTTACACAAACGCCAGCACAAGTTCAACCAGTGTCACATCATCTACACCAACAGTGGT
ATCC

Alignment

ORF - retro_ggor_2853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAWIKRKFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKKKK
          MAWIKRKFG...P.KRLTREAM.NYLK..GDQ.VL.LHAKV.QKSYGNEKRFFCPPPCVYLMGSGWKK.K
Retrocopy MAWIKRKFGKWSPFKRLTREAM*NYLKG*GDQIVLTLHAKVVQKSYGNEKRFFCPPPCVYLMGSGWKKIK

Parental  EQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIG
          .QM..DGCSEQ.SQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISD.DK.KHFMLSVK.FYGN.DDIG
Retrocopy *QMKCDGCSEQGSQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDLDKQKHFMLSVKVFYGNGDDIG

Parental  VFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQW-GAFFIH
          VFLSK.....SKPSKKKQSLKNADLCIASGTKVALFNRL.SQTVSTRYLHVE.GNFH..S.Q..G..F..
Retrocopy VFLSKS----SKPSKKKQSLKNADLCIASGTKVALFNRLLSQTVSTRYLHVERGNFH-ASSQQ>GEHFTL

Parental  LLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDT
          .LDDD.SEGEEFTV.DGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQT.LLDADDPVSQLHKCAF.L.DT
Retrocopy FLDDDGSEGEEFTV*DGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTTLLDADDPVSQLHKCAFDLEDT

Parental  ERMYLCLSQERIIQFQATPCPKEPNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLN
          ER.YLCLSQERIIQFQATPCP.EPNK.MINDGASW.IIST.K..YTFYE.MGPVLA.V.P.PVVESL..N
Retrocopy ERKYLCLSQERIIQFQATPCPTEPNKKMINDGASWAIISTHKGKYTFYERMGPVLALVMPTPVVESLKSN

Parental  GGGDVAMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDG
          GGGD.AMLELTGQNFTPNL.VWFGDVEAE.MYRCGESML.VVPD.SAF.EGWR.V.QPVQV.VTLVRNDG
Retrocopy GGGDEAMLELTGQNFTPNLQVWFGDVEAEAMYRCGESMLRVVPDVSAF*EGWR*VQQPVQVSVTLVRNDG

Parental  IIYSTSLTFTYTPEPGPRPHCSAAGAILRANSSQVPPNESNTNSEGSYTNASTNSTSVTSSTATVVS
          IIYSTSLTFTYTPE.GPRPHCS.AGAIL.A.SS.VPPNE.NTNS.G.YTNAST.STSVTSST.TVVS
Retrocopy IIYSTSLTFTYTPEAGPRPHCSVAGAILQASSSHVPPNELNTNSDGIYTNASTSSTSVTSSTPTVVS

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	0.05 RPM	25.46 RPM
SRP007412_cerebellum	0.00 RPM	26.67 RPM
SRP007412_heart	0.00 RPM	9.60 RPM
SRP007412_kidney	0.00 RPM	29.48 RPM
SRP007412_liver	0.00 RPM	17.46 RPM
SRP007412_testis	0.21 RPM	59.67 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_2853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2853 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,