RetrogeneDB ID: retro_ptro_2621

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:47490054..47490843(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC14B
• Ensembl ID: ENSPTRG00000021155
• Aliases: None
• Description: None

Sequence

>retro_ptro_2621
GCAGTAAAGAAGGCAATGCAGTATGGCTTCCTTAATTTCAACTCATTTAACCTTGATGAATATGAACACTATGAAAAAGC
AGAAAACGGAGATTTAAATTGGATAATACCCGACCGATTTATTGCCTTCTGTGGACCTCATTCAAGAGCCAGACTTGAAA
GTGGTTACCACCAACATTCTCCCGAGACTTATATTCAATATTTTAAGAATCACAATGTTACTACCATTATTCGTCTGAAT
AAAAGGATATATGATGCCAAACGCTTTACGGATGCTGGCTTCGATCACCATGATCTTTTCTTTGCAGATGGCAGCACCCC
TACTCATGCCATTGTCAAAAGACTTCTGGATATCTGTGAAAATGCTGAGGGTGCCATTGCAGTACATTGTAAAGCTGGCC
TTGGTCGCACGGGCACTCTGATAGCCTGCTACATCATGAAGCATTACAGGATGACAGCAGCCGAGACCATTGCATGGGTA
AGGATCTGCAGACCTGGCTTGGTGATCGGGCCTCAGCAGCAGTTTTTGGTGATGAAGCAAACAAGCCTCTGGCTGGAAGG
GGACTATTTTCATCAGAAGTTAAAGGGGCAGGAGAATGGACAACACAGAGCAGCCTTCTCCAAACTTCTCTCCGGTGTTG
ATGACATTTCCATAAATGGGGTCGAGAATCAAGACCAGCAAGAACCCAACCCTTACAGTGATGACGACGAAATCAATGGA
GTGACACAAGGTGATAGAAGTCGGGCCCTGAAAAGGTGAAGACAATCAAAAACAAACGATATTCTTCTC

Alignment

ORF - retro_ptro_2621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.06 %
• Parental protein coverage: 52.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVKKAMQYGFLNFNSFNLDEYEHYEKAENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKN
          AVKKAMQYGFLNFNSFNLDEYEHYEKAENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKN
Retrocopy AVKKAMQYGFLNFNSFNLDEYEHYEKAENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKN

Parental  HNVTTIIRLNKRMYDAKRFTDAGFDHHDLFFADGSTPTDAIVKEFLDICENAEGAIAVHCKAGLGRTGTL
          HNVTTIIRLNKR.YDAKRFTDAGFDHHDLFFADGSTPT.AIVK..LDICENAEGAIAVHCKAGLGRTGTL
Retrocopy HNVTTIIRLNKRIYDAKRFTDAGFDHHDLFFADGSTPTHAIVKRLLDICENAEGAIAVHCKAGLGRTGTL

Parental  IACYIMKHYRMTAAETIAWVRICRPGSVIGPQQQFLVMKQTNLWLEGDYFRQKLKGQENGQHRAAFSKLL
          IACYIMKHYRMTAAETIAWVRICRPG.VIGPQQQFLVMKQT.LWLEGDYF.QKLKGQENGQHRAAFSKLL
Retrocopy IACYIMKHYRMTAAETIAWVRICRPGLVIGPQQQFLVMKQTSLWLEGDYFHQKLKGQENGQHRAAFSKLL

Parental  SGVDDISINGVENQDQQEPEPYSDDDEINGVTQGDRLRALKSRRQSKTNAIPL
          SGVDDISINGVENQDQQEP.PYSDDDEINGVTQGDR.RALK..RQSKTN.I.L
Retrocopy SGVDDISINGVENQDQQEPNPYSDDDEINGVTQGDRSRALKR*RQSKTNDILL

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	0.02 RPM	18.64 RPM
SRP007412_cerebellum	0.00 RPM	6.24 RPM
SRP007412_heart	0.00 RPM	18.39 RPM
SRP007412_kidney	0.00 RPM	35.17 RPM
SRP007412_liver	0.00 RPM	30.64 RPM
SRP007412_testis	2.85 RPM	58.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2621 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2621 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2621 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3845

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000081377	2 retrocopies	retro_hsap_3729, retro_hsap_3845,
Macaca mulatta	ENSMMUG00000005997	1 retrocopy	retro_mmul_1615,
Nomascus leucogenys	ENSNLEG00000016822	1 retrocopy	retro_nleu_1981,
Pongo abelii	ENSPPYG00000019417	1 retrocopy	retro_pabe_208,
Pan troglodytes	ENSPTRG00000021155	2 retrocopies	retro_ptro_2524, retro_ptro_2621 ,
Ictidomys tridecemlineatus	ENSSTOG00000012205	1 retrocopy	retro_itri_1799,
Ictidomys tridecemlineatus	ENSSTOG00000028527	3 retrocopies	retro_itri_1798, retro_itri_1821, retro_itri_1890,