RetrogeneDB ID: retro_ptro_1238

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:64286819..64287407(-)
• Located in intron of: ENSPTRG00000009555

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLIC1
• Ensembl ID: ENSPTRG00000017982
• Aliases: None
• Description: chloride intracellular channel 1 [Source:HGNC Symbol;Acc:2062]

Sequence

>retro_ptro_1238
ATAGCTGAAGAACAACTGCAAGTTGAATTGTTCGTGAAGGCTGGCAGTGATGGGGCCAAGATTGGGAACTGCCCCTTCTC
CTAGAGACTGTTCATGGTGCTGTGGCTCAAGGGAGTCACCTTCAATGTCACCATCATTGACACCAAGAGGCAGACCAAGA
TAGTGCAAAAGCTGTGCCCAGGAGGGCAGCTCCCATTCCTGCTGTATGGCATGGAAGAGCACAAGGACACCAACAAGATT
GAGGAATTTCTGTAGGCAGTGCTGTGCCCTCCTAGGTACCCCAAGCTGGCAGCTCTGAACCCTGAATCCAACACAGCTGA
GCAGGACATATTTGCCAAATTTTCTGCTTACATCAAGAATTCAAACCCAGCACTCAGTGACAATCTGGAGAAGGGACTCC
TGAAAGCCCTGAAGGTTTTAGACAATCACTTGACATCCCGCCACTCAGAAGAAGTGGATGAAACCAGTGCTGAAGATGAA
GGCATCTCTCAGAGGAAGTTTCTGGATGGCAGTGAGCTCACCCTGGCTGACTGCAACCTGTTGCCAACGCTCCACATAGT
ACAAGTGGTGTGTAAGAAGTACCAAGGG

Alignment

ORF - retro_ptro_1238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.27 %
• Parental protein coverage: 81.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEEQPQVELFVKAGSDGAKIGNCPFSQRLFMVLWLKGVTFNVTTVDTKRRTETVQKLCPGGQLPFLLYG
          .AEEQ.QVELFVKAGSDGAKIGNCPFS.RLFMVLWLKGVTFNVT..DTKR.T..VQKLCPGGQLPFLLYG
Retrocopy IAEEQLQVELFVKAGSDGAKIGNCPFS*RLFMVLWLKGVTFNVTIIDTKRQTKIVQKLCPGGQLPFLLYG

Parental  TEVHTDTNKIEEFLEAVLCPPRYPKLAALNPESNTAGLDIFAKFSAYIKNSNPALNDNLEKGLLKALKVL
          .E.H.DTNKIEEFL.AVLCPPRYPKLAALNPESNTA..DIFAKFSAYIKNSNPAL.DNLEKGLLKALKVL
Retrocopy MEEHKDTNKIEEFL*AVLCPPRYPKLAALNPESNTAEQDIFAKFSAYIKNSNPALSDNLEKGLLKALKVL

Parental  DNYLTSPLPEEVDETSAEDEGVSQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRG
          DN.LTS...EEVDETSAEDEG.SQRKFLDG.ELTLADCNLLP.LHIVQVVCKKY.G
Retrocopy DNHLTSRHSEEVDETSAEDEGISQRKFLDGSELTLADCNLLPTLHIVQVVCKKYQG

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	0.07 RPM	7.17 RPM
SRP007412_cerebellum	0.22 RPM	11.15 RPM
SRP007412_heart	0.06 RPM	29.12 RPM
SRP007412_kidney	0.13 RPM	106.05 RPM
SRP007412_liver	0.03 RPM	45.99 RPM
SRP007412_testis	0.00 RPM	14.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1238 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1238 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2153
Pongo abelii	retro_pabe_1514
Macaca mulatta	retro_mmul_1269

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000621	2 retrocopies	retro_cfam_481, retro_cfam_525,
Callithrix jacchus	ENSCJAG00000002788	1 retrocopy	retro_cjac_2972,
Dipodomys ordii	ENSDORG00000016424	3 retrocopies	retro_dord_506, retro_dord_524, retro_dord_550,
Felis catus	ENSFCAG00000019049	1 retrocopy	retro_fcat_1301,
Gorilla gorilla	ENSGGOG00000011331	1 retrocopy	retro_ggor_2153,
Macropus eugenii	ENSMEUG00000015201	1 retrocopy	retro_meug_254,
Macaca mulatta	ENSMMUG00000029827	3 retrocopies	retro_mmul_1269, retro_mmul_290, retro_mmul_902,
Monodelphis domestica	ENSMODG00000015240	1 retrocopy	retro_mdom_1166,
Nomascus leucogenys	ENSNLEG00000006264	3 retrocopies	retro_nleu_1296, retro_nleu_24, retro_nleu_2894,
Oryctolagus cuniculus	ENSOCUG00000022545	1 retrocopy	retro_ocun_1449,
Otolemur garnettii	ENSOGAG00000031840	4 retrocopies	retro_ogar_2402, retro_ogar_3273, retro_ogar_407, retro_ogar_982,
Procavia capensis	ENSPCAG00000013268	1 retrocopy	retro_pcap_30,
Pongo abelii	ENSPPYG00000016456	2 retrocopies	retro_pabe_1514, retro_pabe_886,
Pan troglodytes	ENSPTRG00000000350	3 retrocopies	retro_ptro_2816, retro_ptro_3107, retro_ptro_396,
Pan troglodytes	ENSPTRG00000017982	2 retrocopies	retro_ptro_1238 , retro_ptro_724,
Sarcophilus harrisii	ENSSHAG00000006493	1 retrocopy	retro_shar_28,
Tarsius syrichta	ENSTSYG00000001540	2 retrocopies	retro_tsyr_1452, retro_tsyr_722,