RetrogeneDB ID: retro_ptro_756

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:39973408..39973806(-)
• Located in intron of: ENSPTRG00000004907

Retrocopy information

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

Parental gene information

• Parental gene symbol: FGFR1OP2
• Ensembl ID: ENSPTRG00000004783
• Aliases: None
• Description: None

Sequence

>retro_ptro_756
ATGAGTTGCACAATTGAGAAGGCACTTGCTGATGCTAAAACTCTTGTTGAAAGATTAAGAGATCACGACGATGCAGCAGA
ATCTCTGATTGAGCAAACCACAGCTCTCAACAAGCGAGTAGAAGCCACGAAGCAGTATCAGAAAGAAATTCAAGAGCTTA
ATGAAGTCGCAAGAACATCGGCCACGGTCCACGTTAGTTATGGGAATCCAGCAAGAAAACAGACAAATCAGAGAATTGCA
ACAAGAAAGAAAAGAATTGCGTACATCCCTGGAAGAACATCAGTCGGCCTTGGAACTTACGATGAGCAAGTATCGAGAAC
AAATGGTTAGATTGCTAATGACTAGCAAAAAAGATGATCCGGGAAAAATAATGAAGTTAACAAAAGCAGCACTCCAAG

Alignment

ORF - retro_ptro_756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.04 %
• Parental protein coverage: 52.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSCTIEKALADAKALVERLRDHDDAAESLIEQTTALNKRVEAMKQYQEEIQELNEVAR-HRPRSTLVMGI
          MSCTIEKALADAK.LVERLRDHDDAAESLIEQTTALNKRVEA.KQYQ.EIQELNEVAR.HRPRSTLVMGI
Retrocopy MSCTIEKALADAKTLVERLRDHDDAAESLIEQTTALNKRVEATKQYQKEIQELNEVAR>HRPRSTLVMGI

Parental  QQENRQIRELQQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKL-KEQHSK
          QQENRQIRELQQE.KELRTSLEEHQSALEL.MSKYREQM.RLLM.SKKDDPG.IMKL...QHSK
Retrocopy QQENRQIRELQQERKELRTSLEEHQSALELTMSKYREQMVRLLMTSKKDDPGKIMKL>QKQHSK

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	32.53 RPM
SRP007412_cerebellum	0.29 RPM	29.07 RPM
SRP007412_heart	0.00 RPM	17.81 RPM
SRP007412_kidney	0.16 RPM	23.96 RPM
SRP007412_liver	0.00 RPM	10.77 RPM
SRP007412_testis	0.11 RPM	31.09 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_756 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_756 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_756 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_994
Pongo abelii	retro_pabe_839

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756 ,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608,