RetrogeneDB ID: retro_ptro_2985

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390389.1:3641405..3642076(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC59
• Ensembl ID: ENSPTRG00000009398
• Aliases: None
• Description: None

Sequence

>retro_ptro_2985
ATGACTATTCTCCCGTCGGATTTCTGTGGCCTCACACACCTGGCGAAGCTAGACCTTAGAAAGAACAAGCCACAGCAGCC
ACCAGCAGACTTGGGCCGTTTGGTCAACCTCCAGCACCTGGCTCTCCTCAACAACAGGCTGGTCACCTTGTCGTCAGCTT
TGCTCAGCTGAAGAACCTGAAGTGGCTAGACCTGAAGGATAACCTCTGGATCCCAGCCTGGCCAAGGTGGCAAGTGACTG
CTTGGGTGAGAAGCCATGGAAACAGCATGCAAACAAAGCATCACAACACATGAAGGCTGTACAGGCAGACCACAAGTGGG
AGAGGCAGCAGGGTTGGGAGTAGAACGAGAGACAGAGGAGAAGCATGAGGCAAAGCAGCAAGCTAAGGAAGCTCAGGAGA
GGAAATGCGGAAGCGGGAGAAGGCAGAAGAGAAGGAGTGCCAGAGAAAGGAGTATGATGCCCTCAAAGTAGCCAAGCAGG
AGCAGATGATATCTACCAAGGAAACAAATCAGACCCCCAAATCTAAGTCCGAATCCTGCCCCTGCAAGCCACTCCCCCGG
CAGCACACTCGTTTCTGGGCTGTGCTGAAACTGCTGCTGCTGCTGCTTCTGCTTTGTGCGGCGGGGGTGTTGGTTGCTTG
TCGGGTGACACAGCTACAGCAGCTGCCCCTC

Alignment

ORF - retro_ptro_2985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.43 %
• Parental protein coverage: 73.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LTTLPSDFCGLTHLVKLDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLP-VSFAQLKNLKWLDLKDN-
          .T.LPSDFCGLTHL.KLDL.KNK.QQ.PAD.GRLVNLQHL.LLNN.LVTL..VSFAQLKNLKWLDLKDN.
Retrocopy MTILPSDFCGLTHLAKLDLRKNKPQQPPADLGRLVNLQHLALLNNRLVTLS<VSFAQLKNLKWLDLKDN<

Parental  PLDPVLAKVAGDCLDEKQCKQCANKVLQHMKAVQADQERERQRRLE-VEREAEKKREAKQRAKEAQER-E
          PLDP.LAKVA.DCL.EK..KQ.ANK..QHMKAVQAD...ERQ...E.VERE.E.K.EAKQ.AKEAQER.E
Retrocopy PLDPSLAKVASDCLGEKPWKQHANKASQHMKAVQADHKWERQQGWE<VERETEEKHEAKQQAKEAQER<E

Parental  LRKREKAEEKERRRKEYDALKAAKREQEKKPKKEANQAPKSKSGSRPRKPPPRKHTRSWAVLKLLLLLLL
          .RKREKAEEKE..RKEYDALK.AK.EQ.....KE.NQ.PKSKS.S.P.KP.PR.HTR.............
Retrocopy MRKREKAEEKECQRKEYDALKVAKQEQ-MISTKETNQTPKSKSESCPCKPLPRQHTRXXXXXXXXXXXXX

Parental  FGVAGGLVACRVTELQQQPL
          ...AG.LVACRVT.LQQ.PL
Retrocopy XCAAGVLVACRVTQLQQLPL

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	48.78 RPM
SRP007412_cerebellum	0.00 RPM	43.09 RPM
SRP007412_heart	0.00 RPM	23.23 RPM
SRP007412_kidney	0.00 RPM	49.30 RPM
SRP007412_liver	0.03 RPM	163.61 RPM
SRP007412_testis	0.00 RPM	67.02 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2985 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2985 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2985 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3479
Gorilla gorilla	retro_ggor_2346
Pongo abelii	retro_pabe_2874

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018827	1 retrocopy	retro_cjac_2342,
Equus caballus	ENSECAG00000018072	1 retrocopy	retro_ecab_240,
Homo sapiens	ENSG00000108829	1 retrocopy	retro_hsap_3479,
Gorilla gorilla	ENSGGOG00000006310	1 retrocopy	retro_ggor_2346,
Monodelphis domestica	ENSMODG00000020901	1 retrocopy	retro_mdom_1882,
Nomascus leucogenys	ENSNLEG00000009066	1 retrocopy	retro_nleu_2629,
Pongo abelii	ENSPPYG00000008284	3 retrocopies	retro_pabe_2687, retro_pabe_2874, retro_pabe_2875,
Pan troglodytes	ENSPTRG00000009398	1 retrocopy	retro_ptro_2985 ,
Tarsius syrichta	ENSTSYG00000000371	1 retrocopy	retro_tsyr_25,
Tursiops truncatus	ENSTTRG00000000207	1 retrocopy	retro_ttru_1931,