RetrogeneDB ID: retro_pabe_1592

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:38040668..38041332(-)
• Located in intron of: ENSPPYG00000009077

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM60A
• Ensembl ID: ENSPPYG00000004396
• Aliases: None
• Description: protein FAM60A [Source:RefSeq peptide;Acc:NP_001125318]

Sequence

>retro_pabe_1592
ATGTTTGGTTTTCACAAGCCAAAGATGTACCGAAGTATAGAGGGCTGCTGTATTTGCAGAGCTAAGTCCTCCAGTTCTCG
ATTCACTGACAGTAAACGCTATGAAAAGGACTTCCAGAGCTGTTCTGGATTGCATGAGACTCCTTCAGGAGACATTTGCA
ATGCCTGTGTCCTGCTTGTGAAAAGATGGAAGAAGTTGCCAGCAGGATCAAAAAAAAAACTGGAATCATGTGGTAGATGC
AAGGGCTGGACCCAGTCTAAAGACTACATTGAAACCAAAGAAAGTGAAAACTCCATCTGGGAACAGGATAAAGAGCAACC
GTATCAGTAAACTGCAGAAGGAATTTATACGTAATAATTCTGATGCTCACAGTACCACCTCCAGTGCCTCCCCAGCTCAA
TTTCCTTGTTACAGTAACCAGTCAGATGACGGCTCAGATACAGAGATGGCTTCCGGTTCTAACAGAACACCAGTTTTTTC
CTTTTGAGACCTCACATACTGGAAAAGACAGAAAGCATGTTGTGGGATCATCTATAAAGGCCGTTTTGGGGAAGTCCTCA
TTGACACACATCTCTTCAAGCCTTGCTGCAGCAATAAGAAAGCAGCTGCCGAGAAGCCATAGGAGCAGGGGCCAGAGCCT
CTGCCCATCTCCACTCAGGAGTGG

Alignment

ORF - retro_pabe_1592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFGFHKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAGS
          MFGFHKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSC.GLHET.SGDICNACVLLVKRWKKLPAG.
Retrocopy MFGFHKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCSGLHETPSGDICNACVLLVKRWKKLPAGX

Parental  KKN-WNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQKEFKRHNSDAHSTTSSASPAQSPCYSN
          ....WNHVVDARAGPSLKTTLKPKKVKT.SGNRIKSN.ISKLQKEF.R.NSDAHSTTSSASPAQ.PCYSN
Retrocopy XXX>WNHVVDARAGPSLKTTLKPKKVKTPSGNRIKSNRISKLQKEFIRNNSDAHSTTSSASPAQFPCYSN

Parental  QSDDGSDTEMASGSNRTPVFSFLDLTYWKRQKICCGIIYKGRFGEVLIDTHLFKPCCSNKKAAAEKPEEQ
          QSDDGSDTEMASGSNRTPVFSF.DLTYWKRQK.CCGIIYKGRFGEVLIDTHLFKPCCSNKKAAAEKP.EQ
Retrocopy QSDDGSDTEMASGSNRTPVFSF*DLTYWKRQKACCGIIYKGRFGEVLIDTHLFKPCCSNKKAAAEKP*EQ

Parental  GPEPLPISTQEW
          GPEPLPISTQEW
Retrocopy GPEPLPISTQEW

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	0.94 RPM
SRP007412_cerebellum	0.00 RPM	4.99 RPM
SRP007412_heart	0.03 RPM	8.49 RPM
SRP007412_kidney	0.03 RPM	15.28 RPM
SRP007412_liver	0.00 RPM	3.95 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1592 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1592 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1592 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1928
Gorilla gorilla	retro_ggor_1405

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001161	1 retrocopy	retro_btau_1020,
Canis familiaris	ENSCAFG00000010685	4 retrocopies	retro_cfam_1120, retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Choloepus hoffmanni	ENSCHOG00000007193	17 retrocopies	retro_chof_109, retro_chof_1108, retro_chof_1136, retro_chof_1255, retro_chof_1614, retro_chof_1689, retro_chof_1770, retro_chof_1971, retro_chof_2126, retro_chof_2493, retro_chof_2576, retro_chof_2587, retro_chof_453, retro_chof_511, retro_chof_856, retro_chof_979, retro_chof_998,
Callithrix jacchus	ENSCJAG00000001215	3 retrocopies	retro_cjac_1072, retro_cjac_3154, retro_cjac_3289,
Felis catus	ENSFCAG00000008955	4 retrocopies	retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Homo sapiens	ENSG00000139146	3 retrocopies	retro_hsap_1928, retro_hsap_1945, retro_hsap_4029,
Gorilla gorilla	ENSGGOG00000015484	3 retrocopies	retro_ggor_1405, retro_ggor_1415, retro_ggor_2704,
Myotis lucifugus	ENSMLUG00000009827	3 retrocopies	retro_mluc_1663, retro_mluc_1672, retro_mluc_765,
Macaca mulatta	ENSMMUG00000009155	2 retrocopies	retro_mmul_1074, retro_mmul_2324,
Nomascus leucogenys	ENSNLEG00000016487	1 retrocopy	retro_nleu_1213,
Otolemur garnettii	ENSOGAG00000008927	4 retrocopies	retro_ogar_1253, retro_ogar_1762, retro_ogar_2117, retro_ogar_251,
Pongo abelii	ENSPPYG00000004396	2 retrocopies	retro_pabe_1592 , retro_pabe_3309,
Rattus norvegicus	ENSRNOG00000046048	1 retrocopy	retro_rnor_2858,
Rattus norvegicus	ENSRNOG00000049943	2 retrocopies	retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii	ENSSHAG00000006261	1 retrocopy	retro_shar_670,
Ictidomys tridecemlineatus	ENSSTOG00000007097	1 retrocopy	retro_itri_16,
Tursiops truncatus	ENSTTRG00000008465	3 retrocopies	retro_ttru_1162, retro_ttru_1498, retro_ttru_984,