RetrogeneDB ID: retro_ggor_2595

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:57480890..57482039(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNJ
• Ensembl ID: ENSGGOG00000006034
• Aliases: None
• Description: None

Sequence

>retro_ggor_2595
ATGGAGTTGGAGGGGCAGTGGTGGTGAGGACAGCTGGCCGCCGACATTCACCAAGCACTTCGCTACAGGGAGCTGAAGTT
GCCCTCCTATAAAGGCCAGTCCCCTCAATTAAGTCTCAGACGGTATTTTGCTGACTTGATTTGCCACTGTGAGCAATTGC
TTCCATGCCTTTGCCCTTCTGCCCGCCATCTTGCTGTCTAGTTTACTGGACCTGTTCATGGACCGCTATGACATCTCTAT
CCAGCAGCTGCATTGAGTTGCGCTTTCCTGCCTGCTTCTAGCAAGTAAATTTGAAGAAAAAGAAGAAAGTGTGTCTAAGC
TGGAGCAGCTCAACAGCCTGGGTTGTATGACTAATATGAATCTAGTATTAACAAAACAAAATTTGCTGCATATGGAACTA
TTATTATTAGAAACCTTTCAGTGGAACCCCTGCCTTCCAACAGCCGCCCATTTCATTGAGTATTATCTCTCTGAAGCAGA
ACACAAAACAGATTTTCATGACGGCTGGCCAATGATTTGCTTGGAAAAGACTAAATTCTAAATGGCCAAATATGCAGATT
ACTTCCTGGAAGTATCTTTGTAAGATTACGCCTTTCTAAAGTATGCACCTTTAGTAGCTGCTGCGTATGTGGCTTCTGCG
AGGATTATACTTCGTCTTTCTCCAACGTGGCCTACAAGACTGCATCGTCTTACTGCTTACTCTTGGGATTTCTTAGTGCA
ATGTATTGAACAGCTATTGATCGCTCACGATAATGATGTGAAAGAAGCAAACAAACGGAGAGGGCAAGCAGGACCTCAGT
CAGCACAACCAAGTGTGTTCCAGAAAGCCTCCCAGCCCTCACGGCTAGTTCATTTTCAGCAACCTCAATATCTCCATCAG
ACACCTCAGACCTCACTGCAGTATCGCCATCCTAGTCAGAACAACCAAGCTGTCAGCATATTGTATCGACCACACACACT
TCATCTTACACACTACAGACATGTCCTGCTGGCTTCCAAGCTAGTGTTCAGGGCCTTGGGCACATGCAGACTAGTATTGG
AATGCCACTGGCAATACCAGTAGAAGTTAAGCCCTGTCTGAGTGTTTCTTATAACCGGAGTTATCAGATAAATAAACATT
ACCCTTGTATTACTTCGTGTTTTGAAAGG

Alignment

ORF - retro_ggor_2595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MELEGQWWRGQLAADIHQALRYKELTLPSYKGQSPQLSLRRYFADLIAIVSNRFT-LCPSARHLAV-YLL
          MELEGQWW.GQLAADIHQALRY.EL.LPSYKGQSPQLSLRRYFADLI.........LCPSARHLAV..LL
Retrocopy MELEGQWW*GQLAADIHQALRYRELKLPSYKGQSPQLSLRRYFADLICHCEQLLPCLCPSARHLAV>SLL

Parental  DLFMDRYDISIQQLHLVALSCLLLASKFEEKEDSVPKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETF
          DLFMDRYDISIQQLH.VALSCLLLASKFEEKE.SV.KLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETF
Retrocopy DLFMDRYDISIQQLH*VALSCLLLASKFEEKEESVSKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETF

Parental  QWNLCLPTAAHFIEYYLSEAVHETDLHDGWPMICLEKTKLYMAKYADYFLEVSLQDYAFLNYAPSLVAAA
          QWN.CLPTAAHFIEYYLSEA.H.TD.HDGWPMICLEKTK..MAKYADYFLEVSL.DYAFL.YAP.LVAAA
Retrocopy QWNPCLPTAAHFIEYYLSEAEHKTDFHDGWPMICLEKTKF*MAKYADYFLEVSL*DYAFLKYAP-LVAAA

Parental  CVASSRIILRLSPTWPTRLHRLTAYSWDFLVQCIERLLIAHDNDVKEANKQRGQAGPQSAQLSVFQTASQ
          .VAS.RIILRLSPTWPTRLHRLTAYSWDFLVQCIE.LLIAHDNDVKEANK.RGQAGPQSAQ.SVFQ.ASQ
Retrocopy YVASARIILRLSPTWPTRLHRLTAYSWDFLVQCIEQLLIAHDNDVKEANKRRGQAGPQSAQPSVFQKASQ

Parental  PSRPVHFQQPQYLHQTHQTSLQYRHPT-SEQPSCQQIVSTTHTSSYTLQTCPAGFQTSVQGLGHMQTGVG
          PSR.VHFQQPQYLHQT.QTSLQYRHP..SEQPSCQ.IVSTTHTSSYTLQTCPAGFQ.SVQGLGHMQT..G
Retrocopy PSRLVHFQQPQYLHQTPQTSLQYRHPS<SEQPSCQHIVSTTHTSSYTLQTCPAGFQASVQGLGHMQTSIG

Parental  MSLAIPVEVKPCLSVSYNRSYQINEHYPCITPCFER
          M.LAIPVEVKPCLSVSYNRSYQIN.HYPCIT.CFER
Retrocopy MPLAIPVEVKPCLSVSYNRSYQINKHYPCITSCFER

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	2.35 RPM
SRP007412_cerebellum	0.00 RPM	3.66 RPM
SRP007412_heart	0.00 RPM	0.50 RPM
SRP007412_kidney	0.00 RPM	3.03 RPM
SRP007412_liver	0.00 RPM	1.74 RPM
SRP007412_testis	0.10 RPM	8.29 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_2595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2595 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3850

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016259	1 retrocopy	retro_cjac_3274,
Erinaceus europaeus	ENSEEUG00000002270	2 retrocopies	retro_eeur_535, retro_eeur_577,
Homo sapiens	ENSG00000107443	1 retrocopy	retro_hsap_3850,
Gorilla gorilla	ENSGGOG00000006034	1 retrocopy	retro_ggor_2595 ,
Oryctolagus cuniculus	ENSOCUG00000011114	1 retrocopy	retro_ocun_425,
Tarsius syrichta	ENSTSYG00000009466	1 retrocopy	retro_tsyr_741,