RetrogeneDB ID: retro_ptro_2723

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:141662111..141662552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNHIT1
• Ensembl ID: ENSPTRG00000019525
• Aliases: None
• Description: None

Sequence

>retro_ptro_2723
GTCCACTCCCAGGACCCTGGGCAGCAACGGGTGCTGGACTGGGCCAGCTGGCAGTGACGCATCAACTGGCAGCTAGAAGT
CCTGGAGAATGACAACTTCCAGGACGACCCCCATGTGGGACTCCCTCAGCTCAGCAAGAGACTGCCACAGTTCGATGATG
ATGCAGACACCAGACAGTAAAAGAAGAAAACCCGAGGTGATCATTTTCAACTTCGCTTCCAAAAAAACTTTCAGGCCCTG
CTGGAGGAGCAGAACTTGAGTGTGGCCAAGGGCCCCAACTACCTGATAGCCTGTGCAGAGTCCCTGTCACGGCCACAGCG
CTCCTTCTATGCTGTCTGCGGCTTCCTCTCCCCCTACACCTGTGTCAGCTGTGGTGCCTGGTATTGCACCGTGTGCTGTC
TGGGGACCCACCAGGAGACCAGATGTCTGAAGTGGACCATG

Alignment

ORF - retro_ptro_2723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.31 %
• Parental protein coverage: 95.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRSQDPGQRRVLDRAARQRRINRQLEALENDNFQDDPHAGLPQLGKRLPQFDDDADTGKKKKKTRGDHFK
          V.SQDPGQ.RVLD.A..Q.RIN.QLE.LENDNFQDDPH.GLPQL.KRLPQFDDDADT...KKKTRGDHF.
Retrocopy VHSQDPGQQRVLDWASWQ*RINWQLEVLENDNFQDDPHVGLPQLSKRLPQFDDDADTRQ*KKKTRGDHFQ

Parental  LRFRKNFQALLEEQNLSVAEGPNYLTACAGPPSRPQRPFCAVCGFPSPYTCVSCGARYCTVRCLGTHQET
          LRF.KNFQALLEEQNLSVA.GPNYL.ACA...SRPQR.F.AVCGF.SPYTCVSCGA.YCTV.CLGTHQET
Retrocopy LRFQKNFQALLEEQNLSVAKGPNYLIACAESLSRPQRSFYAVCGFLSPYTCVSCGAWYCTVCCLGTHQET

Parental  RCLKWTV
          RCLKWT.
Retrocopy RCLKWTM

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	31.60 RPM
SRP007412_cerebellum	0.00 RPM	14.84 RPM
SRP007412_heart	0.00 RPM	8.22 RPM
SRP007412_kidney	0.00 RPM	56.91 RPM
SRP007412_liver	0.00 RPM	75.88 RPM
SRP007412_testis	0.21 RPM	11.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2723 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2723 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4012

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010174	1 retrocopy	retro_etel_1701,
Homo sapiens	ENSG00000106400	1 retrocopy	retro_hsap_4012,
Gorilla gorilla	ENSGGOG00000016713	1 retrocopy	retro_ggor_2694,
Macaca mulatta	ENSMMUG00000006951	1 retrocopy	retro_mmul_2315,
Pan troglodytes	ENSPTRG00000019525	1 retrocopy	retro_ptro_2723 ,
Rattus norvegicus	ENSRNOG00000001418	2 retrocopies	retro_rnor_2162, retro_rnor_2278,