RetrogeneDB ID: retro_ggor_2588

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:47064336..47065395(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC4
• Ensembl ID: ENSGGOG00000005420
• Aliases: None
• Description: None

Sequence

>retro_ggor_2588
GACCAGTGGGAAGAGGAATTTGAAAAGGTCCCCCTGTTTATGAAGAAAGTGCCATCAGAAATTGATCCCAGGGAGAATCC
TGACTTGGCTTGTCTCCAGTCAATTATTTTTGATGAGGAGCATTCTCCAGAACAGGCCAAGACCTATAAAGATGAGGGCA
ATGATTATTTTAAAGAAAAAGACTACAAGAAAGCTGTAATTTCCTACACTGAAGGATTAAAGAAGAAATGTGCAAATCCT
GATTTGAATGCTGTCCTTTATACCAACCGGGCAGCAGCACAATACTATCTGGGCAATTTTCATTCTGCTCTCAGTGATGT
GACAGCTGCCAAAAAGTTAAAACCGTGCTACCTCAAAGCAATAATAAGAGGTGCCTTATGCCATCTGGAACTGAAACACT
TTGCCAAGGCTGTGAACTGATGTGATGAGGGACTGCAGATAGATGCCAAAGAGAAGAAGCTTCTGGAAATGAGGGCTAAA
GTAGACAAGCTGAAGCTAATTGAACAGAGGGATGTGAGGAAAGCCAACTTGAAAGAAAAGGAGAGGAATCAGAATGAAGT
TTTACTCCAGGATATCAAGGCTAGGAATATCAGGCTCTCTGAAGCTGCCTGTGAGGATGAAGTTTCAGCCTCAGAAGGTC
TAGGTGAGCTTTTCCTGGATGGACTCAGCTCTGAGAACCCCCATGGAGCCAGACTGAGTCTAGATGACCAGGGCAGGCTG
AGCTGGCCTGTGCTCTTTCTGTACCCAGAGTGTGCCCAATCGGACTTCATCTCTGCTTTTCATGAGGACTCCAGGTTTAT
TGATCATCTAATGGTGATGTTTGGTGAAACACCCTCTTGGGACCTAGAGCAAAAATATTGCCCTGATAATTTGGAGGTCT
ACACTGAGGATGAGGACAGGGCAGAACTGTACTGGGTGCCTGCCAAGAGCACCTTGCTGCAGGATCTACAGCACCACAGG
CACTTTGTAAAAGCCCTGACACCAGCATTTTTGGTCTGTGTAGGATCCAAACTTTTTTGAACGAATTATCTCTGGGGGAG
AAAGGTGCACCAGATAAGA

Alignment

ORF - retro_ggor_2588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 89.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRWFLEFEKVPLFMTRAPSEIDPRENPDLACLQSIIFDEERSPEEQAKTYKDEGNDYFKEKDYKKAVISY
          D.W..EFEKVPLFM...PSEIDPRENPDLACLQSIIFDEE.SPE.QAKTYKDEGNDYFKEKDYKKAVISY
Retrocopy DQWEEEFEKVPLFMKKVPSEIDPRENPDLACLQSIIFDEEHSPE-QAKTYKDEGNDYFKEKDYKKAVISY

Parental  TEGLKKKCADPDLNAVLYTNRAAAQYYLGNFRSALNDVTAARKLKPCHLKAIIRGALCHLELKHFAEAVN
          TEGLKKKCA.PDLNAVLYTNRAAAQYYLGNF.SAL.DVTAA.KLKPC.LKAIIRGALCHLELKHFA.AVN
Retrocopy TEGLKKKCANPDLNAVLYTNRAAAQYYLGNFHSALSDVTAAKKLKPCYLKAIIRGALCHLELKHFAKAVN

Parental  WCDEGLQIDAKEKKLLEMRAKADKLKRIEQRDVRKANLKEKKERNQNEALLQAIKARNIRLSEAACEDED
          .CDEGLQIDAKEKKLLEMRAK.DKLK.IEQRDVRKANLKEK.ERNQNE.LLQ.IKARNIRLSEAACEDE.
Retrocopy *CDEGLQIDAKEKKLLEMRAKVDKLKLIEQRDVRKANLKEK-ERNQNEVLLQDIKARNIRLSEAACEDEV

Parental  SASEGLGELFLDGLSTENPHGARLSLDDQGRLSWPVLFLYPEYAQSDFISAFHEDSRFIDHLMLMFGETP
          SASEGLGELFLDGLS.ENPHGARLSLDDQGRLSWPVLFLYPE.AQSDFISAFHEDSRFIDHLM.MFGETP
Retrocopy SASEGLGELFLDGLSSENPHGARLSLDDQGRLSWPVLFLYPECAQSDFISAFHEDSRFIDHLMVMFGETP

Parental  SWDLEQKYCPDNLEVYFEDEDRAELYRVPAKSTLLQVLQHQRYFVKALTPAFLVCVGSSPFCKNYLQGRK
          SWDLEQKYCPDNLEVY.EDEDRAELY.VPAKSTLLQ.LQH.R.FVKALTPAFLVCVGS..F..NYL.GRK
Retrocopy SWDLEQKYCPDNLEVYTEDEDRAELYWVPAKSTLLQDLQHHRHFVKALTPAFLVCVGSKLF*TNYLWGRK

Parental  VYQIR
          V.QIR
Retrocopy VHQIR

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	6.28 RPM
SRP007412_cerebellum	0.00 RPM	6.46 RPM
SRP007412_heart	0.00 RPM	2.35 RPM
SRP007412_kidney	0.04 RPM	8.46 RPM
SRP007412_liver	0.03 RPM	4.64 RPM
SRP007412_testis	0.10 RPM	17.61 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_2588 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2588 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3843
Pan troglodytes	retro_ptro_2620
Macaca mulatta	retro_mmul_1616

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000005420	1 retrocopy	retro_ggor_2588 ,
Macaca mulatta	ENSMMUG00000006754	1 retrocopy	retro_mmul_1616,
Nomascus leucogenys	ENSNLEG00000003044	1 retrocopy	retro_nleu_1978,