RetrogeneDB ID: retro_ptro_3298

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:24855178..24856412(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSPTRG00000021473
• Aliases: None
• Description: None

Sequence

>retro_ptro_3298
ATATCCAGCAAAGGATCCATGGTTCTGGCCCACAGTGGTGGCCTGGACACCTCCTGCATGCTTGTGTGGCTGAAGGAACA
AGGACATGATGTCACTGCCTACCTGGCCAACATTGGCCAGAAGGAAGACTTTGAGAAAGACAGGAAGAAGGCATGCAAGC
TTGGGGCCAAAAAGGTGTTCATTGAGGATGTCAGCAGGGAGTTTGTGGAGGAGTTCATCTGGCCGGCCATCCAGTCCAGC
ACCCTGTATGAGGACTACTACCTCCTGGGCACCTCTCTGGCTAGGCTCTGCATCGCCCACAAACAAGTGGAAATCACCCA
GCAGGAGGGGGCCAAGTACGTATCCTATGGCATCATGGGAAAGGAGAACGATCATGTCCAGTTTGAGCTCACCTGCTCAC
TGGCCCTCAGATTAAGGTCATTGCTCCCTGGAGGATGCCCGAGTTCTACTACTGGCTCAACGGCTGCAATGATCTGATGG
AATACACAAAGCAACATCGGATTCCCATCCCAGTCACTCTCAAGAACCCGTGGAGCATGGACGAGAACCTCATGTGTATC
AGCTATGAGGCTGGAATCCTGGAGAAACACAAGTACCATAAGCACCTCCCGGTCTCTACACAAAGACTAAGGACCTGACC
AAAGCCCCCAACACCCCTGACATTCTCTAGATTGAGTTCAAAAAAGAGGTCCCCATGAAGGTGACCAACGTCAAGGATGG
CGCCACCCACCAGACCTCCTAGGAGCTCTGCGTGTACCTGAACGAAGCTGCAAGCAAGCATGGCCTGGGCCATATTGACA
TCATGGAGAACCATTTCATTGCAATGAAGTCCTGAGGCATCTATGAGACCCCAGCAGGCACCATCCTTTACCATGCTCAT
TTACACATCCAGGCCTTCACCATGAATCAGGAAGAGTGCAAAATCAAACAAGGCCTGGGCTTGAAATTTGCTGCGCTGGT
GTACACCAGTTTCTGGCACAGCCCTGAATGTGAATTTGTCCACCACTGCATCACCAAGTCCCAGGAGTGAGTGGAAGGGA
AAGTGCAGGTGTCTGTCTTCAAGAGCCAGGTGGACATCCTCAGACAGGAGTCCCCACTGTCTCTCTAAAATGAGGAGCTG
GTGAGCATGAATGTGCAGGGCGATTAGGAGCCAATTAATGCCACCAGGTTCATCTACATCAATTCCATCAGGCTGAAGGA
ATATCATTGTCTCTAAAGCAAGCTCCCTGCCAAA

Alignment

ORF - retro_ptro_3298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSKEFVE
          .SSKGS.VLA.SGGLDTSC.LVWLKEQG.DV.AYLANIGQKEDFE..RKKA.KLGAKKVFIEDVS.EFVE
Retrocopy ISSKGSMVLAHSGGLDTSCMLVWLKEQGHDVTAYLANIGQKEDFEKDRKKACKLGAKKVFIEDVSREFVE

Parental  EFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELSCYSLA-PHI
          EFIWPAIQSS.LYED.YLLGTSLAR.CIA.KQVEI.Q.EGAKYVS.G..GK.ND.V.FEL.C.SLA.P.I
Retrocopy EFIWPAIQSSTLYEDYYLLGTSLARLCIAHKQVEITQQEGAKYVSYGIMGKENDHVQFELTC-SLA<PQI

Parental  KVIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTK
          KVIAPWRMPEFY....G.NDLMEY.KQH.IPIPVT.KNPWSMDENLM.ISYEAGILE..K........T.
Retrocopy KVIAPWRMPEFYYWLNGCNDLMEYTKQHRIPIPVTLKNPWSMDENLMCISYEAGILEKHKYHKHLPVSTQ

Parental  TQDPAKAPNTP-DILEIEFKKGVP-VKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMK
          .......P.TP........KK..P..KVTNVKDG.THQTS.EL..YLNE.A.KHG.G.IDI.EN.FI.MK
Retrocopy RLRT*PKPPTPLTFSRLSSKKRSP<MKVTNVKDGATHQTS*ELCVYLNEAASKHGLGHIDIMENHFIAMK

Parental  SRGIYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEG
          S.GIYETPAGTILYHAHL.I.AFTM..E..KIKQGLGLKFA.LVYT.FWHSPECEFV.HCI.KSQE.VEG
Retrocopy S*GIYETPAGTILYHAHLHIQAFTMNQEECKIKQGLGLKFAALVYTSFWHSPECEFVHHCITKSQE*VEG

Parental  KVQVSVLKGQVYILGRESPLSLYNEELVSMNVQGDYEPTDATGFININSLRLKEYHRLQSKVTAK
          KVQVSV.K.QV.IL..ESPLSL.NEELVSMNVQGD.EP..AT.FI.INS.RLKEYH.L.SK..AK
Retrocopy KVQVSVFKSQVDILRQESPLSL*NEELVSMNVQGD*EPINATRFIYINSIRLKEYHCL*SKLPAK

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	0.02 RPM	42.11 RPM
SRP007412_cerebellum	0.04 RPM	48.83 RPM
SRP007412_heart	0.00 RPM	16.26 RPM
SRP007412_kidney	0.05 RPM	1168.07 RPM
SRP007412_liver	0.00 RPM	933.12 RPM
SRP007412_testis	0.00 RPM	18.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3298 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3298 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3298 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4648
Homo sapiens	retro_hsap_4934

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219, retro_cjac_4038, retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298 , retro_ptro_571, retro_ptro_762,