RetrogeneDB ID: retro_ptro_1996

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:73215418..73215979(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNDC9
• Ensembl ID: ENSPTRG00000012278
• Aliases: None
• Description: None

Sequence

>retro_ptro_1996
ATGGAAGCTGATGCATCTGTTGACATGTTTTCCAAAGTCCTGGAGAATCAGCTGCTTCAGACTACCAAACTGGTGGAAGA
ACATTTGGATTCTGAAATTCAAAAACTGGATCAGATGGATGAGGATGAACTGGAACACATTAAAGAAAAGAGACTCGAGG
CACTAAGGAAAGCTCAACAGCAGAAACAAGAATGGCTTTCTAAAGGACATGGGGAATACAGAGAAATCCCTAGTGAAAGA
GACTTTTTTCAAGAAGTCAAGGAGAGTAAAAAAGTGGTTTGCCATTTCTACAGAGACTCCACATTCAGGTGTAAAATACT
AGACAGATTTCTGGCGATATTGTCCGAGAAACACCTCGAGACCAAATTTTTGAAGCTGAATGTGGAAAAAGCACCTTTCC
TTTGTGAGAGACTGCATATCAAAGTCATTCCCACACTAGCACTGGTAAAAGATGGGAAAGCACAAGATTATGTTGTTGGG
TTTACTGACCTAGGAAATACAGATGACTTCACCACAGAAACTTTAGAATGGGGGCTCAGTTGTTCTGACATTCTTAATTA
C

Alignment

ORF - retro_ptro_1996 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.51 %
• Parental protein coverage: 82.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEADASVDMFSKVLEHQLLQTTKLVEEHLDSEIQKLDQMDEDELERLKEKRLQALRKAQQQKQEWLSKGH
          MEADASVDMFSKVLE.QLLQTTKLVEEHLDSEIQKLDQMDEDELE..KEKRL.ALRKAQQQKQEWLSKGH
Retrocopy MEADASVDMFSKVLENQLLQTTKLVEEHLDSEIQKLDQMDEDELEHIKEKRLEALRKAQQQKQEWLSKGH

Parental  GEYREIPSERDFFQEVKESENVVCHFYRDSTFRCKILDRHLAILSKKHLETKFLKLNVEKAPFLCERLRI
          GEYREIPSERDFFQEVKES..VVCHFYRDSTFRCKILDR.LAILS.KHLETKFLKLNVEKAPFLCERL.I
Retrocopy GEYREIPSERDFFQEVKESKKVVCHFYRDSTFRCKILDRFLAILSEKHLETKFLKLNVEKAPFLCERLHI

Parental  KVIPTLALLKDGKTQDYVVGFTDLGNTDDFTTETLEWRLGSSDILNY
          KVIPTLAL.KDGK.QDYVVGFTDLGNTDDFTTETLEW.L..SDILNY
Retrocopy KVIPTLALVKDGKAQDYVVGFTDLGNTDDFTTETLEWGLSCSDILNY

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	6.74 RPM
SRP007412_cerebellum	0.00 RPM	4.27 RPM
SRP007412_heart	0.00 RPM	6.03 RPM
SRP007412_kidney	0.00 RPM	10.62 RPM
SRP007412_liver	0.00 RPM	7.46 RPM
SRP007412_testis	0.00 RPM	10.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1996 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1996 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3042
Gorilla gorilla	retro_ggor_2096

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009936	1 retrocopy	retro_cjac_500,
Dipodomys ordii	ENSDORG00000013557	1 retrocopy	retro_dord_141,
Homo sapiens	ENSG00000115514	1 retrocopy	retro_hsap_3042,
Gorilla gorilla	ENSGGOG00000024615	1 retrocopy	retro_ggor_2096,
Myotis lucifugus	ENSMLUG00000008110	1 retrocopy	retro_mluc_717,
Mus musculus	ENSMUSG00000058407	2 retrocopies	retro_mmus_2791, retro_mmus_873,
Pan troglodytes	ENSPTRG00000012278	1 retrocopy	retro_ptro_1996 ,