RetrogeneDB ID: retro_ptro_652

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:128589599..128590228(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAK1
• Ensembl ID: ENSPTRG00000018053
• Aliases: None
• Description: None

Sequence

>retro_ptro_652
ATGGCATCGGGGCAAGGCCCAGGGCCTCCCAGGCAGGAGTGCGGAAAGCCTGCCCTGCCCTCTGCTTCTGAGGAGCAGGT
AGCCCAGGACATGGAGGGGTTTTCCGCAGCTACGTTTTTTACCACCATCAGCAGGAACAGGAGGCTGAAGGGGCGGCCGC
CCCTGCCAACCCAGAGATGGTCACCTTGCCCCTCCAACCTAGCAGCACCATGGGGCAGGTGGGACGGCAGCTCGCCATCA
CCAGGATGACATCAACCGGCACTATGACTTCGGAGTTCCAGACCATGCTGCAGCACCTGCAGCCCACGGCAGAGAACGCC
TACGAGTACTTCACCAAGATCGCCTCCAGCCTGTTTGAGAGTGGCATCAACCAGGGCCGTGTGGTGGCTCTCCTGGGCTT
CGGCTACCGTCTGGTCCTACATGTCTACCAGCACAGCTTGACTGGCTTCCTGGGCCTGGTGACCCGCTTCGTGGTCTTCA
TGCTGCAACACGGCATCACCCAGTGGATCTCGCAGAGGGGCGGCTGGGTGGCAGCCCTGGACTTGGGCAATAGTCCCATC
CTGAACGTGCTGGTGGTTGTGGGTGTGGTTCTGCTGGGCCAGTTTGTGGTAAGAAGATTCTTCAAATCA

Alignment

ORF - retro_ptro_652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASGQGPGPPRQECGEPALPSASEEQVAQDTEE-VFRSYVFYRHQQEQEAEGAAAPADPEMVTLPLQPSS
          MASGQGPGPPRQECG.PALPSASEEQVAQD.E..VFRSYVFY.HQQEQEAEGAAAPA.PEMVTLPLQPSS
Retrocopy MASGQGPGPPRQECGKPALPSASEEQVAQDMEG<VFRSYVFYHHQQEQEAEGAAAPANPEMVTLPLQPSS

Parental  TMGQVGRQLAIIG-DDINRRYD-SEFQTMLQHLQPTAENAYEYFTKIATSLFESGINWGRVVALLGFGYR
          TMGQVGRQLAI...DDINR.YD.SEFQTMLQHLQPTAENAYEYFTKIA.SLFESGIN.GRVVALLGFGYR
Retrocopy TMGQVGRQLAITR<DDINRHYD>SEFQTMLQHLQPTAENAYEYFTKIASSLFESGINQGRVVALLGFGYR

Parental  LALHVYQHGLTGFLGQVTRFVVDFMLHHCIARWIAQRGGWVAALNLGNGPILNVLVVLGVVLLGQFVVRR
          L.LHVYQH.LTGFLG.VTRFVV.FML.H.I..WI.QRGGWVAAL.LGN.PILNVLVV.GVVLLGQFVVRR
Retrocopy LVLHVYQHSLTGFLGLVTRFVV-FMLQHGITQWISQRGGWVAALDLGNSPILNVLVVVGVVLLGQFVVRR

Parental  FFKS
          FFKS
Retrocopy FFKS

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	10.15 RPM
SRP007412_cerebellum	0.00 RPM	8.75 RPM
SRP007412_heart	0.00 RPM	13.84 RPM
SRP007412_kidney	0.00 RPM	19.17 RPM
SRP007412_liver	0.00 RPM	11.20 RPM
SRP007412_testis	0.00 RPM	2.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_652 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_652 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_942
Gorilla gorilla	retro_ggor_761
Macaca mulatta	retro_mmul_1130

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013657	1 retrocopy	retro_fcat_202,
Homo sapiens	ENSG00000030110	2 retrocopies	retro_hsap_2468, retro_hsap_942,
Gorilla gorilla	ENSGGOG00000022462	1 retrocopy	retro_ggor_761,
Macaca mulatta	ENSMMUG00000009104	1 retrocopy	retro_mmul_1130,
Nomascus leucogenys	ENSNLEG00000008351	1 retrocopy	retro_nleu_296,
Ochotona princeps	ENSOPRG00000001127	2 retrocopies	retro_opri_105, retro_opri_938,
Pan troglodytes	ENSPTRG00000018053	1 retrocopy	retro_ptro_652 ,