RetrogeneDB ID: retro_pabe_3263

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:71421336..71421751(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459K1410
• Ensembl ID: ENSPPYG00000000787
• Aliases: None
• Description: tropomyosin alpha-3 chain [Source:RefSeq peptide;Acc:NP_001126994]

Sequence

>retro_pabe_3263
CTCAACTCCCTGGAGGCGGTGAAACGCAAGATCCAGGCCCTGCAGCAGCAGGCAGAGGAGGCGGAAGACCGCGCAGGGCC
TGCAGCGGGAGCTGGACGGCGAGCGGGAGCGGCGCGAGAAAGCTGAAGGTGATGTGGCCGCCCTCAACCGACGCATCCAG
CTCCTTGAGGAGGAGTTGGACAGGGCTCAGGAACGACTGGCCACAGCCCTGCAGAAGCTGGAGGAGGCAGAAAAAGCTGC
AGATGAGAGTGAGAGAGGAATGAAGGTGATAGAAAACCGGGCCATCAAGGATGAGGAGAAGATGGAGATTCAGGAGATGC
AGCTCAAAGAGGCCAAGCACACTGCGGAAAAGGCTGACCGCAAATACGAGGAGGTAGCTCCTAAGCTGGTCATCCTGGAG
GGTGAGCTGAAGAGG

Alignment

ORF - retro_pabe_3263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 56.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ITTIEAVKRKIQVLQQQADDAEE-RAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERLAT
          ....EAVKRKIQ.L.QQ.....E..A..LQRE..GER..RE.AE..VA.LNRRIQL.EEELDRAQERLAT
Retrocopy LNSLEAVKRKIQAL-QQQAEEAE>TAQGLQRELDGERERREKAEGDVAALNRRIQLLEEELDRAQERLAT

Parental  ALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDLER
          ALQKLEEAEKAADESERGMKVIENRA.KDEEKME.QE.QLKEAKH.AE.ADRKYEEVA.KLVI.EG.L.R
Retrocopy ALQKLEEAEKAADESERGMKVIENRAIKDEEKMEIQEMQLKEAKHTAEKADRKYEEVAPKLVILEGELKR

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	6.30 RPM	202.03 RPM
SRP007412_cerebellum	14.23 RPM	68.95 RPM
SRP007412_heart	9.06 RPM	28.30 RPM
SRP007412_kidney	10.21 RPM	97.22 RPM
SRP007412_liver	9.09 RPM	59.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3263 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3263 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3969
Pan troglodytes	retro_ptro_2694
Gorilla gorilla	retro_ggor_2665

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921, retro_nleu_922,
Otolemur garnettii	ENSOGAG00000025133	1 retrocopy	retro_ogar_62,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263 ,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318, retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,