RetrogeneDB ID: retro_pabe_2248

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:114895695..114896242(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025875
• Aliases: None
• Description: None

Sequence

>retro_pabe_2248
CAGGAGCAAGAAAAACTGTCTTCTGGAGTTATCTGTGTAGGTCACATACCTCCAATGCTTTATGAAACCCAGATCTGAGC
ATATTTCTCCAAGTATGACATGATTACAAGATTCAAGCTCTCCAGAAGTGGAAAGCCTGAAAATGCCAAAACTATGCTTT
TGTGGAGTTTGAGTCTAATGATATTGCGAAGATAGGTGCCAAAACAATGAACCACCTTTTTGGTAAAAGACTCTTCAAGT
GTTATTTTATACCACTTGAAAAAGTACATGAAGAACTTTTCAGAGAGTGGAATGTTCCATGTAAAAAGCCATCATATCCA
GTGAAATGAAACAGTCAGAATTGAACACTTTTAGAAAAGCTGCAGATAAGGAGCTATTTGAAAAGAAAGAAAAATTACTC
AGGAAGAGAATAGCCAAGAAAGAAATTGATTATAATTTTCTTTCACTGATTTAACAGACAGAGGAAAAAAGAAATGTTTC
GAACACTGACTTTCAGAAATCTGCAAATTGTGTTTTACCTAAGAAGAAGAAAAAGGAAATTTTAGGC

Alignment

ORF - retro_pabe_2248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 70.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKQEHLTPGVVYVRHLPNLLNETQIFSYFSQFGTVTRFRLSRSKRTGNSK-GYAFVEFESEDVAKIVAET
          ..QE.L..GV..V.H.P..L.ETQI..YFS.....TRF.LSRS....N.K..YAFVEFES.D.AKI.A.T
Retrocopy QEQEKLSSGVICVGHIPPMLYETQI*AYFSKYDMITRFKLSRSGKPENAK<NYAFVEFESNDIAKIGAKT

Parental  MNNYLFGERLLKCHFMPPEKVHKELFKDWNIPFKQPSYPSVKRYNRNRTLTQKLRM-EERFKKKERLLRK
          M.N.LFG.RL.KC.F.P.EKVH.ELF..WN.P.K.PSYP.VK....N.TL..KL....E.F.KKE.LLRK
Retrocopy M-NHLFGKRLFKCYFIPLEKVHEELFREWNVPCKKPSYP-VK*NSQN*TLLEKLQI<KELFEKKEKLLRK

Parental  KLAKKGIDYDFPSLILQKTE--SISKTNRQTSTKGQVLRKKKKKVSG
          ..AKK.IDY.F.SLI.Q..E....S.T..Q.S.......KKKK...G
Retrocopy RIAKKEIDYNFLSLI*QTEEKRNVSNTDFQKSANCVLPKKKKKEILG

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	6.14 RPM
SRP007412_cerebellum	0.00 RPM	9.48 RPM
SRP007412_heart	0.00 RPM	5.69 RPM
SRP007412_kidney	0.00 RPM	8.62 RPM
SRP007412_liver	0.00 RPM	9.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2248 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2248 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1544

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019387	1 retrocopy	retro_btau_1516,
Choloepus hoffmanni	ENSCHOG00000002227	5 retrocopies	retro_chof_1061, retro_chof_1449, retro_chof_1735, retro_chof_236, retro_chof_2480,
Callithrix jacchus	ENSCJAG00000013386	1 retrocopy	retro_cjac_3076,
Dasypus novemcinctus	ENSDNOG00000005017	2 retrocopies	retro_dnov_1869, retro_dnov_2487,
Erinaceus europaeus	ENSEEUG00000008535	3 retrocopies	retro_eeur_530, retro_eeur_550, retro_eeur_91,
Homo sapiens	ENSG00000155438	5 retrocopies	retro_hsap_1077, retro_hsap_1596, retro_hsap_1609, retro_hsap_1611, retro_hsap_553,
Gorilla gorilla	ENSGGOG00000023498	4 retrocopies	retro_ggor_1213, retro_ggor_1923, retro_ggor_2225, retro_ggor_850,
Loxodonta africana	ENSLAFG00000030731	1 retrocopy	retro_lafr_500,
Microcebus murinus	ENSMICG00000015787	1 retrocopy	retro_mmur_990,
Myotis lucifugus	ENSMLUG00000006481	2 retrocopies	retro_mluc_1217, retro_mluc_1369,
Macaca mulatta	ENSMMUG00000020928	11 retrocopies	retro_mmul_1444, retro_mmul_1544, retro_mmul_2149, retro_mmul_2151, retro_mmul_2225, retro_mmul_2226, retro_mmul_2389, retro_mmul_690, retro_mmul_696, retro_mmul_697, retro_mmul_752,
Monodelphis domestica	ENSMODG00000000152	2 retrocopies	retro_mdom_1271, retro_mdom_737,
Nomascus leucogenys	ENSNLEG00000001163	4 retrocopies	retro_nleu_1756, retro_nleu_1942, retro_nleu_2022, retro_nleu_669,
Pongo abelii	ENSPPYG00000025875	2 retrocopies	retro_pabe_2248 , retro_pabe_510,
Pan troglodytes	ENSPTRG00000012419	5 retrocopies	retro_ptro_1072, retro_ptro_1077, retro_ptro_1080, retro_ptro_1378, retro_ptro_415,
Pteropus vampyrus	ENSPVAG00000016707	1 retrocopy	retro_pvam_134,
Sorex araneus	ENSSARG00000006252	1 retrocopy	retro_sara_362,
Tupaia belangeri	ENSTBEG00000001123	4 retrocopies	retro_tbel_1731, retro_tbel_3479, retro_tbel_4589, retro_tbel_926,
Vicugna pacos	ENSVPAG00000005847	2 retrocopies	retro_vpac_136, retro_vpac_265,