RetrogeneDB ID: retro_ptro_2333

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:28283551..28284658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IQCB1
• Ensembl ID: ENSPTRG00000015281
• Aliases: None
• Description: None

Sequence

>retro_ptro_2333
AATGTCCAAATAGGATCAGCACTCATGATGATGCTACAGAATATACTATAGAGCAACAGTGGTGATTTACTCAGAACAGG
AGGAAAAGCCCTGCATTCAATTTTAGATGAAGTTATTTTCAAGCTTTTTTCAACTCCTAGTCCAGTCATAAGAAGTACTG
CTGCAAAACTCCTACTGTTGATGGCTGAATCCTATCAGGAAATTTTGATTTTACTGAGACAAAGTGCCTGCTACAAAGGA
CTCAGAAGTCTACTAAGTAAACAGGAAACTGGGACAGAATTCAGTCAAGAACTTAGACAGCTCATTGGCCTTTTAAGCCC
AACGGTCTATCAGGAAGTAGAAAACCAGAAACTACATCAAGCAGCATGCTTGATTCAAGCCTATTGGAAGGGTTTTCAGA
CAAGAAAGAGATTAAAGAAGCTTCCATCTGCTGTGATTGCTTTGCAGAGGAGTTTCAGATCTAAACGAACAAAGATGTTG
CTGGAGATAAATAGGAAGAAGGAAGAAGAGGACCTCAGATTGCGATTGCAACTTCAAAGACAGAGAGCCATGAGACTTTC
CCAAGAATTGTGGCTGAGTATGCTCAAAGTAGTTCATCCAGGTCAAGTGGAGAAACACAATAGGGAAATGGAAGAGAAAT
CAGCACTGATTATCCAGAAACATTGGAGAGGGTACAGGGAAAGGAAAAATTTTTGCCAACAGAGGCAGTCTCTCACAGAA
TATAAAGCAGCTGTCATACTTCAAAGAGCAGTGTTTAAATTCCTAGCAAAGTGCCGTAAGAAACAGAAACTATTTGTTCC
TTGGTGAGGACTCCAATGACTCACTGATGCATGCTGAGCTGAACTGAAGCAACAAGCAGATGACTATGTCAGAAGACATT
CGGGCTCTCCAATGTCAGATGTGGTCAGTAGGGAGCCTCATGCCCGAGCTTAAGAACGACTGCAACACTACTTTATGGGC
AGGGCCCTGGAAGAGTGAGCCCAGCAACACAGAGAAGCTCTGATGGTACAGATCAGCACTAACGTTGAACAGCTAATGAA
GGCACCAAGTCTGAAGGAAGCAGAAGGGAAAGAACCTGAGCTCTTCCTAAGATCCAGGCCTGTGGCA

Alignment

ORF - retro_ptro_2333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 61.87 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVQIGSAVMMMLQNILQINSGDLLRIGRKALYSILDEVIFKLFSTPSPVIRSTATKLLLLMAESHQEILI
          NVQIGSA.MMMLQNIL..NSGDLLR.G.KAL.SILDEVIFKLFSTPSPVIRSTA.KLLLLMAES.QEILI
Retrocopy NVQIGSALMMMLQNIL*SNSGDLLRTGGKALHSILDEVIFKLFSTPSPVIRSTAAKLLLLMAESYQEILI

Parental  LLRQSTCYKGLRRLLSKQETGTKFSQELRQLVGLLSPMVYQEVEEQKLHQAACLIQAYWKGFQTRKRLKK
          LLRQS.CYKGLR.LLSKQETGT.FSQELRQL.GLLSP.VYQEVE.QKLHQAACLIQAYWKGFQTRKRLKK
Retrocopy LLRQSACYKGLRSLLSKQETGTEFSQELRQLIGLLSPTVYQEVENQKLHQAACLIQAYWKGFQTRKRLKK

Parental  LPSAVIALQRSFRSKRSKMLLEINRQKEEEDLKLQLQLQRQRAMRLSRELQLSMLEIVHPGQVEKHYREM
          LPSAVIALQRSFRSKR.KMLLEINR.KEEEDL.L.LQLQRQRAMRLS.EL.LSML..VHPGQVEKH.REM
Retrocopy LPSAVIALQRSFRSKRTKMLLEINRKKEEEDLRLRLQLQRQRAMRLSQELWLSMLKVVHPGQVEKHNREM

Parental  EEKSALIIQKHWRGYRERKNFHQQRQSLIEYKAAVTLQRAALKFLAKCRKKKKLFAPWRGLQELTDARRV
          EEKSALIIQKHWRGYRERKNF.QQRQSL.EYKAAV.LQRA..KFLAKCRKK.KLF.PW.GLQ.LTDA...
Retrocopy EEKSALIIQKHWRGYRERKNFCQQRQSLTEYKAAVILQRAVFKFLAKCRKKQKLFVPW*GLQ*LTDAC*A

Parental  ELKKQVDDYVRRHLGSPMSDVVSRELHAQAQERLQHYFMGRALEERAQQHREALMAQISTNVEQLMKAPS
          ELK.Q.DDYVRRH.GSPMSDVVSRE.HA.A.ERLQHYFMGRALEE.AQQHREALM.QISTNVEQLMKAPS
Retrocopy ELKQQADDYVRRHSGSPMSDVVSREPHARA*ERLQHYFMGRALEE*AQQHREALMVQISTNVEQLMKAPS

Parental  LKGAEGKEPELFLSRSRPVA
          LK.AEGKEPELFL.RSRPVA
Retrocopy LKEAEGKEPELFL-RSRPVA

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	0.00 RPM	8.26 RPM
SRP007412_cerebellum	0.00 RPM	12.51 RPM
SRP007412_heart	0.00 RPM	5.13 RPM
SRP007412_kidney	0.00 RPM	7.22 RPM
SRP007412_liver	0.00 RPM	3.21 RPM
SRP007412_testis	0.21 RPM	28.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2333 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2333 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3441
Gorilla gorilla	retro_ggor_2324
Pongo abelii	retro_pabe_2845

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000173226	1 retrocopy	retro_hsap_3441,
Gorilla gorilla	ENSGGOG00000028124	1 retrocopy	retro_ggor_2324,
Otolemur garnettii	ENSOGAG00000004271	1 retrocopy	retro_ogar_3056,
Pongo abelii	ENSPPYG00000013494	1 retrocopy	retro_pabe_2845,
Pan troglodytes	ENSPTRG00000015281	1 retrocopy	retro_ptro_2333 ,