RetrogeneDB ID: retro_ggor_2924

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:70940085..70940969(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPHS1
• Ensembl ID: ENSGGOG00000003806
• Aliases: None
• Description: None

Sequence

>retro_ggor_2924
ATGTCTAAGCGGGAGTCCTTTAACCTGGAAAGTTATGAATTGGACAAAAGCTTCTGGCTAACCAGATTCACTGAACTGAA
GGGCACAGTTGCAAAGTGCCCCAAGATGTCTTGCAAAAATTGCTGGAATCTTTACAGGAGAACCACTTCCAAGAAGACGA
GCAGTTTCTGGGAGCCGTTATGCCAAGGCTTCGCATTGGAATGGATACTTGTGCCATTCCTTTGAGGCACAGTGGGCTTT
CCTTGGTTCAAACCACAGATTACATTTACCCGATCGTAGACGACCCTTACATGATGGGCAGGATAGCATGTGCAAATGTC
CTCAGTGACCTCTATGCAATGGGGGTCACAGAATGTGACAATATGCCGATGCTCCTTGGAGTCAGTAATAAAATGACCGA
CAGGGAAAGGGATAAAGTGATGCCTCTGATTATCCAAAGTTTTAAAGACACAGCTGAGGAAGCAGGAATGTCTGTAATGG
GCAGCCAAACAGTACTAAATCCCTGGATTGTCCTGGGAGGAGTCACTACCACTGTCTTCCAGCCCAATGAATTTATCATG
CCAGACAATGCAGTGCCAGGGGACGTGCTGGTGTTGACAAAACCCCTGGGGACACAGGTGGCAGTGGCTGTGCACCAGTG
GCTGGATATTCCTTAGAAATGGAATAAGATTAAACTAGTGGTCACCGAAGATGTAGAGCTGGCCAACCAGGAGGCGATGA
TGAACATGGTGAGGCTCAACAGGACAGCTGCAGGACTCATGCACACGTTCAATGCCCACATGGCCACTGACATCACGGGC
TTCGGGATTTTGGGCCATGTGCAGAACCTAGCCAAGCAGCAGAGGAACGAGGTGTCATTTGTAATTCACAACCTCCTGGT
GCTG

Alignment

ORF - retro_ggor_2924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.85 %
• Parental protein coverage: 75.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTRESFNPESYELDKSFRLTRFTELKGT-GCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLGIGMD
          MS.RESFN.ESYELDKSF.LTRFTELKGT..CKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRL.IGMD
Retrocopy MSKRESFNLESYELDKSFWLTRFTELKGT<SCKVPQDVLQKLLESLQENHFQEDEQFLGAVMPRLRIGMD

Parental  TCVIPLRHGGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMLMLLGVSNKMTDRERDK
          TC.IPLRH.GLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNM.MLLGVSNKMTDRERDK
Retrocopy TCAIPLRHSGLSLVQTTDYIYPIVDDPYMMGRIACANVLSDLYAMGVTECDNMPMLLGVSNKMTDRERDK

Parental  VMPLIIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMP---VFGFRMVLAGLPSTEIII
          VMPLIIQ.FKD.AEEAG.SV.G.QTVLNPWIVLGGV.TTV.QPNEFIMP...V.G...VL.....T....
Retrocopy VMPLIIQSFKDTAEEAGMSVMGSQTVLNPWIVLGGVTTTVFQPNEFIMPDNAVPGDVLVLTKPLGTQVAV

Parental  PLHSFFSLLEEWLKIAISLFQYVISLTSKKGVFSQSRPLSLPAAGLMHTFNAHAATDITGFGILGHAQNL
          ..H........W.KI.......V..L..........R.L...AAGLMHTFNAH.ATDITGFGILGH.QNL
Retrocopy AVHQWLDIP*KWNKIKLVVTEDV-ELANQEAMMNMVR-LNRTAAGLMHTFNAHMATDITGFGILGHVQNL

Parental  AKQQRNEVSFVIHNLPVL
          AKQQRNEVSFVIHNL.VL
Retrocopy AKQQRNEVSFVIHNLLVL

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	1.01 RPM	15.20 RPM
SRP007412_cerebellum	0.79 RPM	19.11 RPM
SRP007412_heart	0.38 RPM	6.82 RPM
SRP007412_kidney	1.47 RPM	33.49 RPM
SRP007412_liver	0.92 RPM	14.24 RPM
SRP007412_testis	1.55 RPM	19.48 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_2924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2924 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3126
Pongo abelii	retro_pabe_3652

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009494	2 retrocopies	retro_cjac_166, retro_cjac_2219,
Gorilla gorilla	ENSGGOG00000003806	2 retrocopies	retro_ggor_147, retro_ggor_2924 ,
Myotis lucifugus	ENSMLUG00000001971	2 retrocopies	retro_mluc_2350, retro_mluc_728,
Macaca mulatta	ENSMMUG00000021233	4 retrocopies	retro_mmul_1607, retro_mmul_2495, retro_mmul_2647, retro_mmul_922,
Monodelphis domestica	ENSMODG00000016864	1 retrocopy	retro_mdom_86,
Nomascus leucogenys	ENSNLEG00000012205	7 retrocopies	retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Pteropus vampyrus	ENSPVAG00000002945	2 retrocopies	retro_pvam_115, retro_pvam_566,
Rattus norvegicus	ENSRNOG00000018125	1 retrocopy	retro_rnor_59,