RetrogeneDB ID: retro_ptro_2853

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:97403721..97404467(+)
• Located in intron of: ENSPTRG00000021177

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT7
• Ensembl ID: ENSPTRG00000019080
• Aliases: SEPT7, CDC10
• Description: Pan troglodytes septin 7 (SEPT7), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001197121]

Sequence

>retro_ptro_2853
AGTATCATCTCACTTATTGCCACAGAAGACACACTCACACCAGAGGAATGCTAACAGTTTAAAAAACAGATAATGAAAGA
AATCCAAGAACATAAAATTAAAATATATGAATTTCTGGAAACATAATAGAGAAGAAAATAAACTTGTTAAAAAGATAAAG
GACCATTTACCTGTTGGTGTAGTAGGTAGTAATACTATCATCGAAGTTAATGGCAAAATGATCAGAGGAAAGCAGCATCC
TTGGGGTATTGCTGAAGTTGAAAATTGTGAACATTGTGATTTTACAATTCTAAGAAATATGTTGATAAGAACACACATGC
AGGACTTGAAAGAGGTTACTAATAATGTCCACTATGAGAACTACAGAAGCAGAAAACTGGCAGCTGTGACTTATAATGGA
ACTGATAACAACAAGAATAAAGGGCAGCTGACCAAGAGCCCTCCGGCACAAATGGAAGAAGAAAGAAGGGAGCATGTAGC
TAAAATGAAGAAGACGGAGATGGAGATGGAGCAGGTGTTTGAGATGAAGGTCAAAGAAAAAGTTCAAAACTGAAGAACTC
TGAAGCTGAGCTCCAGCAGCACCATGAGCAAATGAAAAGGAATTTGGAAGCACAGCATAAACAATAAGAGGAAAAACGTC
ATCAGTTAGAGGATGAGAAAGCAAACTGGGAAGCTCAACAACGTATTTTAGAACAACGAACTCTTCGAGAACCTTGGAAA
AGAACAAGAAGAAAGAAAGATCTTTT

Alignment

ORF - retro_ptro_2853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83. %
• Parental protein coverage: 57.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NIIPLIAKADTLTPEECQQFKKQIMKEIQEH-KIKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIE
          .II.LIA..DTLTPEEC.QFKKQIMKEIQEH.K.K...F......EENKLVKKIKD.LP..VVGSNTIIE
Retrocopy SIISLIATEDTLTPEEC*QFKKQIMKEIQEH>KLKYMNFWK-HNREENKLVKKIKDHLPVGVVGSNTIIE

Parental  VNGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAAVTYNGVDNNK
          VNGK..RG.Q.PWG.AEVEN.EHCDFTILRNMLIRTHMQDLK.VTNNVHYENYRSRKLAAVTYNG.DNNK
Retrocopy VNGKMIRGKQHPWGIAEVENCEHCDFTILRNMLIRTHMQDLKEVTNNVHYENYRSRKLAAVTYNGTDNNK

Parental  NKGQLTKSPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQ-KLKDSEAELQRRHEQMKKNLEAQHK
          NKGQLTKSP.AQMEEERREHVAKMKK.EMEMEQVFEMKVKEKVQ.KLK.SEAELQ..HEQMK.NLEAQHK
Retrocopy NKGQLTKSPPAQMEEERREHVAKMKKTEMEMEQVFEMKVKEKVQ<KLKNSEAELQQHHEQMKRNLEAQHK

Parental  ELEEKRRQFEDEKANWEAQQRILEQQ-NSSRTLEKNKKKGKIF
          ..EEKR.Q.EDEKANWEAQQRILEQ..NSSRTLEKNKKK...F
Retrocopy Q*EEKRHQLEDEKANWEAQQRILEQR<NSSRTLEKNKKKERSF

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	0.04 RPM	197.21 RPM
SRP007412_cerebellum	0.07 RPM	131.13 RPM
SRP007412_heart	0.03 RPM	101.46 RPM
SRP007412_kidney	0.00 RPM	55.81 RPM
SRP007412_liver	0.00 RPM	27.82 RPM
SRP007412_testis	0.00 RPM	103.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2853 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2853 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4202
Gorilla gorilla	retro_ggor_2816
Pongo abelii	retro_pabe_3438

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Echinops telfairi	ENSETEG00000015624	3 retrocopies	retro_etel_1263, retro_etel_282, retro_etel_517,
Homo sapiens	ENSG00000122545	2 retrocopies	retro_hsap_3810, retro_hsap_4202,
Gorilla gorilla	ENSGGOG00000001175	1 retrocopy	retro_ggor_2816,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Nomascus leucogenys	ENSNLEG00000001673	1 retrocopy	retro_nleu_2152,
Otolemur garnettii	ENSOGAG00000006015	1 retrocopy	retro_ogar_1193,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438,
Pan troglodytes	ENSPTRG00000016192	1 retrocopy	retro_ptro_2753,
Pan troglodytes	ENSPTRG00000019080	2 retrocopies	retro_ptro_2585, retro_ptro_2853 ,
Rattus norvegicus	ENSRNOG00000006545	9 retrocopies	retro_rnor_1424, retro_rnor_1425, retro_rnor_1426, retro_rnor_1427, retro_rnor_1428, retro_rnor_1431, retro_rnor_1445, retro_rnor_1446, retro_rnor_821,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258,
Ictidomys tridecemlineatus	ENSSTOG00000021378	3 retrocopies	retro_itri_1332, retro_itri_1736, retro_itri_1771,