RetrogeneDB ID: retro_ptro_1066

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:63223296..63223865(-)
• Located in intron of: ENSPTRG00000007186

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB14
• Ensembl ID: ENSPTRG00000016311
• Aliases: None
• Description: None

Sequence

>retro_ptro_1066
AGGTTTTGTGAAGTTGATATAACTCCAGAAGACTTGTTTAATATATTTTTTGGGGGTGGATTTCCTTCAGGTAGTATACA
TTCTTTTTCAAATGGAAGAGCTGGTTATAGCCAACAACATCAGCATTGACATAGTGGACATGAAAGAGAAGAGGAAAGAG
GAGATGGAGGTTTTTCTGTGTTTATCCAGCTGATGCCCATAATTGTATTGATCCTCGTGTCATTATCAAGCCAGTTGATG
GTCTGTAATCCTCCTTATTCCTTATATCCCAGATCTGGAACAGGGCAAACTATTGAAACGCAGACAGAAAACTTGGGTGT
TGTTTATTATGTCAGCAAGGACTTTAAAAATGATATAAAGGAATGTTACTACAAAAGGCAGAAAAGAGTGTGGAGGAAGA
TTATGTGACTAATATTCGAAATAACTGCTGGAAAGAAAGACAACAAAAAACAGATATGCAGTATGCAGCAAAAGTATACC
GTGATGATCGACTCCGAAGGAAGGCAGATGCCTTGAGCATGGACAACTGTAAAGAATTAGAGCGGCTTACCGGTCTTTAT
AAAGGAGGA

Alignment

ORF - retro_ptro_1066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.19 %
• Parental protein coverage: 50.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGCEADITPEDLFNIFFGGGFPSGSVHSFSNGRAGYSQQHQHRHSGHEREEERGDGGFSVFIQLMPIIVL
          R.CE.DITPEDLFNIFFGGGFPSGS.HSFSNGRAGYSQQHQH.HSGHEREEERGDGGFSVFIQLMPIIVL
Retrocopy RFCEVDITPEDLFNIFFGGGFPSGSIHSFSNGRAGYSQQHQH*HSGHEREEERGDGGFSVFIQLMPIIVL

Parental  ILVSLLSQLMVSNPPYSLYPRSGTGQTIKMQTENLGVVYYVNKDFKNE-YKGMLLQKVEKSVEEDYVTNI
          ILVSL.SQLMV.NPPYSLYPRSGTGQTI..QTENLGVVYYV.KDFKN..YKGMLLQK.EKSVEEDYVTNI
Retrocopy ILVSLSSQLMVCNPPYSLYPRSGTGQTIETQTENLGVVYYVSKDFKND<YKGMLLQKAEKSVEEDYVTNI

Parental  RNNCWKERQQKTDMQYAAKVYRDDRLRRKADALSMDNCKELERLTSLYKGG
          RNNCWKERQQKTDMQYAAKVYRDDRLRRKADALSMDNCKELERLT.LYKGG
Retrocopy RNNCWKERQQKTDMQYAAKVYRDDRLRRKADALSMDNCKELERLTGLYKGG

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	0.16 RPM	13.07 RPM
SRP007412_cerebellum	0.25 RPM	18.89 RPM
SRP007412_heart	0.17 RPM	6.30 RPM
SRP007412_kidney	0.08 RPM	10.49 RPM
SRP007412_liver	0.03 RPM	4.45 RPM
SRP007412_testis	0.21 RPM	3.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1066 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1066 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1583
Pongo abelii	retro_pabe_1304

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012468	1 retrocopy	retro_acar_144,
Homo sapiens	ENSG00000164031	1 retrocopy	retro_hsap_1583,
Monodelphis domestica	ENSMODG00000020687	2 retrocopies	retro_mdom_1398, retro_mdom_752,
Nomascus leucogenys	ENSNLEG00000013668	2 retrocopies	retro_nleu_1761, retro_nleu_2409,
Otolemur garnettii	ENSOGAG00000005340	1 retrocopy	retro_ogar_120,
Pongo abelii	ENSPPYG00000014956	3 retrocopies	retro_pabe_1304, retro_pabe_982, retro_pabe_983,
Pan troglodytes	ENSPTRG00000002613	1 retrocopy	retro_ptro_1608,
Pan troglodytes	ENSPTRG00000016311	1 retrocopy	retro_ptro_1066 ,
Ictidomys tridecemlineatus	ENSSTOG00000021338	1 retrocopy	retro_itri_1840,