RetrogeneDB ID: retro_ptro_68

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:14191868..14192492(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000012699
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSPTRG00000014693
• Aliases: None
• Description: None

Sequence

>retro_ptro_68
ATGTCCAGTGATAGGCAAAGGTCCGATGATGAGAGCCCCAGCACCAGCAGTGGCAGTTCAGATGCGGACCAGCGAGACCC
AGCCGCTCCAGAGCCTGAAGAACAAGAGGAAAGAAAACCTTCTGCCACCCAGCAGAAGAAAAACACCAAACTCTCTAGCA
AAACCACTGCTAAGTTATCCACTAGTGCTAAAAGAATTCAGAAGGAGCTAGCTGAAATAACCCTTGATCCTCCTGCTAAT
TGCAGTGCTGGGCCTAAAGGAGATAACATTTGTGAATGGAGATCAACTATACTTGGTCCACTGGGTTCTGTATATGAAGG
TGGTGTGTTTTTTCTGGATATCACATTTTCATCAGATTATCCATTTAAGCCACCAAAGGTTACTTTCCGCACCAGAATCT
ATCACTGCAACATCAACAGTCAGGGAGTCATCTGTCTGGACATCCTTAAAGACAACTGGAGTCCCGCTTTGACTATTTCA
AAGGTTTTGCTGTCTATTTGTTCCCTTTTAATGGACTGCAACCCTGTGGATCCTCTGGTTGGAAGCATAGCCACTCAGTA
TTTGACCAACAGAGCAGAACACGACAGGATAGCCAGACAGAGGACCAAGAGATACGCAACATAA

Alignment

ORF - retro_ptro_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.12 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDDDSRASTSSSSSSSSNQQTEKETNTPKKKESKVSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGP
          SD.D.R............Q...K...T..KK..K.S.SK....LSTSAKRIQKELA.ITLDPP.NCSAGP
Retrocopy SDADQR---DPAAPEPEEQEERKPSATQQKKNTKLS-SKTTAKLSTSAKRIQKELAEITLDPPANCSAGP

Parental  KGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSP
          KGDNI.EWRSTILGP.GSVYEGGVFFLDITF...YPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSP
Retrocopy KGDNICEWRSTILGPLGSVYEGGVFFLDITFSSDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSP

Parental  ALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
          ALTISKVLLSICSLL.DCNP.DPLVGSIATQY.TNRAEHDR.ARQ.TKRYAT
Retrocopy ALTISKVLLSICSLLMDCNPVDPLVGSIATQYLTNRAEHDRIARQRTKRYAT

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	0.07 RPM	31.28 RPM
SRP007412_cerebellum	0.00 RPM	27.82 RPM
SRP007412_heart	0.00 RPM	26.70 RPM
SRP007412_kidney	0.00 RPM	31.23 RPM
SRP007412_liver	0.00 RPM	15.65 RPM
SRP007412_testis	0.00 RPM	24.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_68 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_68 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_68 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4653
Gorilla gorilla	retro_ggor_76
Pongo abelii	retro_pabe_3614

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Loxodonta africana	ENSLAFG00000004150	1 retrocopy	retro_lafr_320,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Otolemur garnettii	ENSOGAG00000007527	3 retrocopies	retro_ogar_2029, retro_ogar_2566, retro_ogar_626,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Pan troglodytes	ENSPTRG00000014693	1 retrocopy	retro_ptro_68 ,
Pan troglodytes	ENSPTRG00000017303	3 retrocopies	retro_ptro_26, retro_ptro_3141, retro_ptro_341,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,