RetrogeneDB ID: retro_pabe_2976

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:88058075..88058906(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCN1
• Ensembl ID: ENSPPYG00000003385
• Aliases: None
• Description: reticulocalbin 1, EF-hand calcium binding domain [Source:HGNC Symbol;Acc:9934]

Sequence

>retro_pabe_2976
CGGGCGCTGCGGGCCAAGCCCACCGTGCGCAAGGAGCGCGTGGTGCGGCCTGACTCGGAGCTGGGCGAGCGGCTCCCAGA
GGTCAACCAGAGCTTCCAGTACTGCCATGAGGCCTTCCTGGGCAAGGAGGACTCTAAGACCTTCGGCCGGCTCACCCCGG
ACAAGAGCAAGGAGAGGCTGGGGAAGATTGTTGATCGAATCAACAATGATGGAGATGGCTTTGTCACTACTGAGGAGCTG
AAAACCTGGATCAAACGGGTGCAGAAAAGATACATCTTCGATAATGTCGCCAAAGTCTGGCGGGATTACGATAGGGACAA
GGATGATAAAATTTACTAGGAAGAATACAAACAAGCCACCTGTGACCTAGGAAACCCCGCAGAGTTTCATGATTCTTCAG
TTCATCACACCTTTAAAAAGATGCTGCCACGTGAGGAGAGAAGATTCAAAGCTGCAGACCTCGATGGTGCCCTGACAGCC
ACTCAGGAGGAGTTCACTGCCTTTCTGCATCCTGAAGAGTTTGAGCATATGAAGGAAATTGTGGTTTTGGAAACCCTGGA
GGACAACGACAAGAACGGGGATGGGTTTGTGGATCGGGATGAATATATTGTGGATATGTTTTCCCATGAGGAGAATGGCT
CTGAGCCAGACTGGGTTTTATCAGAACGGGAGCAATTTAACGAATTCCGGGATCTGAACAAGGACTGGAAGTTGGACAAA
GACGAGGTTCGCCACTGGATCCTCCCTCAAGATTATGATCATGCACAGGGTGAGGCCAGGCATCTAGTATATGAGTCAGA
CAAAAACAAGGATGAGAGGCTAAAGAGGAAA

Alignment

ORF - retro_pabe_2976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.17 %
• Parental protein coverage: 84.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVLRAKPTVRKERVVRPDSELGERPPEDNQSFKYDHEAFLGKEDSKTFDQLTPDESKQRLGKIVDRIDND
          R.LRAKPTVRKERVVRPDSELGER.PE.NQSF.Y.HEAFLGKEDSKTF..LTPD.SK.RLGKIVDRI.ND
Retrocopy RALRAKPTVRKERVVRPDSELGERLPEVNQSFQYCHEAFLGKEDSKTFGRLTPDKSKERLGKIVDRINND

Parental  GDGFVTTEELKTWIKRVQKRYIFDNVAKVWKDYDRDKDDKISWEEYKQATYGYYLGNPAEFHDSSDHHTF
          GDGFVTTEELKTWIKRVQKRYIFDNVAKVW.DYDRDKDDKI..EEYKQAT....LGNPAEFHDSS.HHTF
Retrocopy GDGFVTTEELKTWIKRVQKRYIFDNVAKVWRDYDRDKDDKIY*EEYKQATCD--LGNPAEFHDSSVHHTF

Parental  KKMLPRDERRFKAADLNGDLTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNGDGFVDQDEYIADMFS
          KKMLPR.ERRFKAADL.G.LTAT.EEFTAFLHPEEFEHMKEIVVLETLED.DKNGDGFVD.DEYI.DMFS
Retrocopy KKMLPREERRFKAADLDGALTATQEEFTAFLHPEEFEHMKEIVVLETLEDNDKNGDGFVDRDEYIVDMFS

Parental  HEENGPEPDWVLSEREQFNEFRDLNKDGKLDKDEIRHWILPQDYDHAQAEARHLVYESDKNKDEKLTKE
          HEENG.EPDWVLSEREQFNEFRDLNKD.KLDKDE.RHWILPQDYDHAQ.EARHLVYESDKNKDE.L...
Retrocopy HEENGSEPDWVLSEREQFNEFRDLNKDWKLDKDEVRHWILPQDYDHAQGEARHLVYESDKNKDERLKRK

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	0.22 RPM	35.05 RPM
SRP007412_cerebellum	0.00 RPM	21.77 RPM
SRP007412_heart	0.00 RPM	16.20 RPM
SRP007412_kidney	0.00 RPM	31.32 RPM
SRP007412_liver	0.00 RPM	30.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2976 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2976 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2976 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3629

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000049449	2 retrocopies	retro_hsap_1259, retro_hsap_3629,
Pongo abelii	ENSPPYG00000003385	1 retrocopy	retro_pabe_2976 ,
Pongo abelii	ENSPPYG00000017982	1 retrocopy	retro_pabe_211,
Rattus norvegicus	ENSRNOG00000013452	28 retrocopies	retro_rnor_1207, retro_rnor_1224, retro_rnor_2111, retro_rnor_2112, retro_rnor_2113, retro_rnor_2352, retro_rnor_2353, retro_rnor_2354, retro_rnor_2355, retro_rnor_2408, retro_rnor_2409, retro_rnor_2410, retro_rnor_2434, retro_rnor_2435, retro_rnor_2436, retro_rnor_2437, retro_rnor_2438, retro_rnor_2486, retro_rnor_2508, retro_rnor_2509, retro_rnor_2510, retro_rnor_2511, retro_rnor_2513, retro_rnor_2664, retro_rnor_2711, retro_rnor_2716, retro_rnor_2760, retro_rnor_797,