RetrogeneDB ID: retro_ptro_1052

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:42117880..42118724(-)
• Located in intron of: ENSPTRG00000007024

Retrocopy information

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

Parental gene information

• Parental gene symbol: AZI2
• Ensembl ID: ENSPTRG00000014707
• Aliases: None
• Description: 5-azacytidine induced 2 [Source:HGNC Symbol;Acc:24002]

Sequence

>retro_ptro_1052
AGAGATGATTTAAAGAGCAAATTGGATAAAATGAGTAAACACAACTCTGAATCTTTAAAAGTATTGAATAAACAGATGCA
ATCTAAAGAAGGAGAACTCTAGCTAAGGACAGAGGTCGAAACTCAGCTGGTGATGAGGAATTTCAATCCACCTTCATCAA
ACTGGGAGGTGGAAAAGTTAAGCTGTGACCTGAAGATCCACGGTTTGGAACAAGAGTTGATGAGGAAAGAAGGTAACGAT
CTCAAAATAGAACTACTCAAAAACCAGACAAACCTATCTGTATGAGGAAGACAATCTTGAAGAGCAGAGATCTCTGAAGA
GTAAGAACTTCAAGTGATAATACACAGAATGTATACTGGCAACTGAAGAGATAAATGTCTAATTTATATCTGGTGACTCA
AGTGCTAGCTGAACTATTAAGAAAACTGGAAACCCCAACTGCAATCAAGAAAGCCTGCACCTCGGTAGGATGCATTGAAG
ACCCTTGGAAAGACAGCACAAAACTGCGCATGATGAATTTTACTGCAACATACACAAGACATCCCCTTCTCTCACCAAAT
GGCAAAGTTCTTTTTTATACTACATCTTCCCCTTTACCAGGAGATATAAAGGTTTTATCAGAGAAAGCAGTCCTCCAATC
ATGGACAGATAATGAGAGAGCCATTCCTAATGAGGGCACACACTCTTACGGCAGAAATTCTCTGGAAGATCATTTTGAGT
ATTCCCAATCCCTCCTGACTCAAGTGAGACAGCATTTAGGGAAATTAAAGTAAAATTTTGCCTTCTAACCAATGTGCCAC
TACTGCATTACTTGGATCAACATAATAAAAATTTCCTTTATAAG

Alignment

ORF - retro_ptro_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.32 %
• Parental protein coverage: 73.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RDNLKSKLDKMNKDNSESLKVLNEQLQSKEVELLQLRTEVETQQVMRNLNPPSSNWEVEKLSCDLKIHGL
          RD.LKSKLDKM.K.NSESLKVLN.Q.QSKE.EL..LRTEVETQ.VMRN.NPPSSNWEVEKLSCDLKIHGL
Retrocopy RDDLKSKLDKMSKHNSESLKVLNKQMQSKEGEL*-LRTEVETQLVMRNFNPPSSNWEVEKLSCDLKIHGL

Parental  EQELELMRKECSDLKIEL-QKAKQTDPYQEDNL-KSRDLQKLSISSDNMQHAYWELKREMSNLHLVTQVQ
          EQEL..MRKE..DLKIEL..K..QT..Y.EDNL.KSRDL.....SSDN.Q..YW.LKR.MSNL.LVTQV.
Retrocopy EQEL--MRKEGNDLKIEL>SKTRQTYLYEEDNL>KSRDL*RVRTSSDNTQNVYWQLKR*MSNLYLVTQVL

Parental  AELLRKLKTSTAIKKACAPVGCSEDLGRDSTKLHLMNFTATYTRHPPLLPNGKALCHTTSSPLPGDVKVL
          AELLRKL.T.TAIKKAC..VGC.ED...DSTKL..MNFTATYTRHP.L.PNGK.L..TTSSPLPGD.KVL
Retrocopy AELLRKLETPTAIKKACTSVGCIEDPWKDSTKLRMMNFTATYTRHPLLSPNGKVLFYTTSSPLPGDIKVL

Parental  SEKAILQSWTDNERSIPNDGTCFQEHSSYGRNSLEDNSW-VFPSPPKSSETAFGETKTKTLPLPNLPPLH
          SEKA.LQSWTDNER.IPN.GT....HS.YGRNSLED....VFP.PP.SSETAF.E.K.K...L.N.P.LH
Retrocopy SEKAVLQSWTDNERAIPNEGT----HS-YGRNSLEDHFE<VFPIPPDSSETAFREIKVKFCLLTNVPLLH

Parental  YLDQHNQNCLYK
          YLDQHN.N.LYK
Retrocopy YLDQHNKNFLYK

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	20.18 RPM
SRP007412_cerebellum	0.00 RPM	23.95 RPM
SRP007412_heart	0.00 RPM	14.17 RPM
SRP007412_kidney	0.00 RPM	26.39 RPM
SRP007412_liver	0.00 RPM	11.10 RPM
SRP007412_testis	0.11 RPM	30.14 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1052 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1052 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1052 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010432	2 retrocopies	retro_chof_1794, retro_chof_234,
Dasypus novemcinctus	ENSDNOG00000011053	2 retrocopies	retro_dnov_1377, retro_dnov_542,
Homo sapiens	ENSG00000163512	2 retrocopies	retro_hsap_1491, retro_hsap_1564,
Gorilla gorilla	ENSGGOG00000022881	2 retrocopies	retro_ggor_1145, retro_ggor_1189,
Loxodonta africana	ENSLAFG00000008538	2 retrocopies	retro_lafr_529, retro_lafr_925,
Myotis lucifugus	ENSMLUG00000000043	3 retrocopies	retro_mluc_1707, retro_mluc_435, retro_mluc_611,
Macaca mulatta	ENSMMUG00000000056	1 retrocopy	retro_mmul_2135,
Monodelphis domestica	ENSMODG00000015075	1 retrocopy	retro_mdom_1786,
Nomascus leucogenys	ENSNLEG00000004069	1 retrocopy	retro_nleu_1714,
Oryctolagus cuniculus	ENSOCUG00000014956	1 retrocopy	retro_ocun_1778,
Otolemur garnettii	ENSOGAG00000005896	1 retrocopy	retro_ogar_3078,
Pongo abelii	ENSPPYG00000014053	2 retrocopies	retro_pabe_1241, retro_pabe_3784,
Pan troglodytes	ENSPTRG00000014707	1 retrocopy	retro_ptro_1052 ,
Tursiops truncatus	ENSTTRG00000016434	1 retrocopy	retro_ttru_1093,