RetrogeneDB ID: retro_ptro_348

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:140077991..140079269(-)
• Located in intron of: ENSPTRG00000001596

Retrocopy information

• Ensembl ID: ENSPTRG00000040188
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZC3H15
• Ensembl ID: ENSPTRG00000012717
• Aliases: None
• Description: None

Sequence

>retro_ptro_348
ATGCCCCCCAAGAAACAGGCTCAGGCCAGGGGCAGCAAAAAGGCGGAGCAAAAAAAGAAGGAGAAGATTATCGAAGACAA
AACTTTCGGTTTGAAGAATAAGAAAGGAGCAAAGCAACAGAAGTTTATCAAGGCTGTCACACATCAAGTTAAATTTGGTC
AACAAAATCCACGTCAGGTAGCACAGAGTGAAGCTGAAAAGAAATTGAAGAAGGATGACAAGAAGAAAGAATTGCAGGAG
CTAAATGAGCTGTTCAAACCTGTAGTTGCTGCTCAAAAAATAAGTAAAGGTGCAGATCCCAAGTCTGTAGTATGTGCATT
CTTCAAGCAACGACAGTGTACTAAAGGAGATAAGTGTAAGTTCTCCCATGACTTGACTCTGGAGAGAAAATGTGAAAAGC
GAAGTGTTTACATTGATGCAAGAGATGAAGAACTTGAAAAAGATACTATGGATAATTGGGATGAGAAAAAGCTGGAAGAA
GTAGTGAACAAGAAGCACGGTGAGGCGGAAAAGAAAAAACCAAAAACTCAAATAGTGTGCAAGCATTTCCTGGAAGCTAT
TGAAAACAACAAGTATGGCTGGTTTTGGGTATGCCCTGGAGGGGGTGATATTTGCATGTATCGTCACGCACTTCCTCCTG
GATTTGTGTTGAAAAAAGATAAAAAGAAAGAAGAGAAAGAAGATGAAATTTCATTAGAAGATCTAATTGAGAGAGAGCAT
TCTGCCCTAGGTCCAAATGTTACCAAAATCACTCTAGAATCTTTTCTTGCCTGGAAGAAAAGGAAAAGACAAGAAAAGAT
TGATAAACTTGAACAAGATATGGAAAGAAGGAAAGCTGACTTCAAAGCAGGGAAAGCACTAGTGATCAGTGGTCGTGAAG
TGTTTGAATTTCGTCCTGAACTGGTCAATGATGATGATGAGGAAGCAGATGATACCCGCTACACCCAGGGAACAGGTGGT
GATGAGGTGGATGATTCAGTGAGTGTAAATGACATAGATTTAAGCCTGTACATCCCAAGAGATGTAGATGAAACAGGTAT
TACCATAGCCAGTCTTGAAAGATTCAGCACATATACTTCAGATAAAGATGAAAACAAATTAAGTGAAGCTTCTGGAGGTA
GGGCTGAAAATGGTGAAAGAAGTGACTTGGAAGAGGACAACGAGAGGGAGGGACCGGAAAATGGAGCCATTGATGCTGTT
CCTGTTGATGAAAATCTTTTCACTGGAGAGGATTTGGATGAACTAGAAGAGGAATTAAATACACTTGATTTAGAAGAA

Alignment

ORF - retro_ptro_348 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
          MPPKKQAQA.GSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
Retrocopy MPPKKQAQARGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK

Parental  KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLERKCEKRSVYIDA
          KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQ.QCTKGDKCKFSHDLTLERKCEKRSVYIDA
Retrocopy KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQRQCTKGDKCKFSHDLTLERKCEKRSVYIDA

Parental  RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGWFWVCPGGGDICMYRHA
          RDEELEKDTMDNWDEKKLEEVVNKKHGEA.......QIVCKHFLEAIENNKYGWFWVCPGGGDICMYRHA
Retrocopy RDEELEKDTMDNWDEKKLEEVVNKKHGEAXXXXXXXQIVCKHFLEAIENNKYGWFWVCPGGGDICMYRHA

Parental  LPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKAD
          LPPGFV..............SLEDLIERE.SALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKAD
Retrocopy LPPGFVXXXXXXXXXXXXXXSLEDLIEREHSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKAD

Parental  FKAGKALVISGREVFEFRPELVNDDDEEADDTRYTQGTGGDEVDDSVSVNDIDLSLYIPRDVDETGITVA
          FKAGKALVISGREVFEFRPELVNDDDEEADDTRYTQGTGGDEVDDSVSVNDIDLSLYIPRDVDETGIT.A
Retrocopy FKAGKALVISGREVFEFRPELVNDDDEEADDTRYTQGTGGDEVDDSVSVNDIDLSLYIPRDVDETGITIA

Parental  SLERFSTYTSDKDENKLSEASGGRAENGERSDLEEDNEREGPENGAIDAVPVDENLFTGEDLDELEEELN
          SLERFSTYTSDKDENKLSEASGGRAENGERSDLEEDNEREGPENGAIDAVPVDENLFTGEDLDELEEELN
Retrocopy SLERFSTYTSDKDENKLSEASGGRAENGERSDLEEDNEREGPENGAIDAVPVDENLFTGEDLDELEEELN

Parental  TLDLEE
          TLDLEE
Retrocopy TLDLEE

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	0.68 RPM	32.10 RPM
SRP007412_cerebellum	0.07 RPM	23.44 RPM
SRP007412_heart	0.12 RPM	16.44 RPM
SRP007412_kidney	0.18 RPM	21.68 RPM
SRP007412_liver	0.07 RPM	15.32 RPM
SRP007412_testis	0.21 RPM	34.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_348 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_348 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348 ,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,