RetrogeneDB ID: retro_pabe_1440

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:19573176..19573941(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK3
• Ensembl ID: ENSPPYG00000007239
• Aliases: None
• Description: mitogen-activated protein kinase 3 [Source:HGNC Symbol;Acc:6877]

Sequence

>retro_pabe_1440
TACGTGGTCCTGGACCTGATGGAAAGCGACCTCCACCAGATCATCCACTCCTCACAGCCCCTCACACTGGAACACGTGCG
CTACTTCTTGTACCAACTGCTGCGGGGCCTGAAGTACATGCACTCGGCTCAGGTCATCCACCGTGACCTCAAGCCTTCCA
ACCTATTGGTGAATGAGAACTGTGAGCTGAAGATTGGTGACTTTGGTATGGCTCGTGGCCTGTGCACCTCGCCCGCTGAA
CATCAGTACTTCATGACTGAGTATGTGGCCACGCGCTGGTACCGTGCACCCGAGCTCATGCTCTCTTTGCATGAGTATAC
ACAGGCTATTGACCTCTGGTCTGTGGGCTGCATCTTTGGTGAGATGCTGGCCCGGCGCCAGCTCTTCCCAGGCAAAAACT
ACGTACACCAGCTACAGCTCATCATGATGGTGCTGGGTACCCCATCACCAGCTGTGATTCAGGCTGTGGGGGCTGAGAGG
GTGCGGGCCTATATCCAGAGCTTGCCACCACGCCAGCCTGTGCCCTGGGAGACAGTGTACCCAGGTGCCGACCGCCAGGC
CCTATCACTGCTGGGTCGCATGCTGCGTTTTGAGCCCAGCGCCCGCATCTCAGCAGCTGCTGCCCTTCGCCACCCTTTCC
TGGCCAAGTACCATGATCCTGATGATGAGCCTGACTGTGCCCCGCCCTTTGACTTTGCTTTTGACCGTGAAGCCCTCACT
CGGGAGCGCATTAAGGAGGCCATTGTGGCTGAAATTGAGGACTTC

Alignment

ORF - retro_pabe_1440 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.55 %
• Parental protein coverage: 66.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YIVQDLMETDLYKLLKSQQ-LSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGL
          Y.V.DLME.DL.....S.Q.L...H..YFLYQ.LRGLKY.HSA.V.HRDLKPSNLL.N..C.LKI.DFG.
Retrocopy YVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGM

Parental  AR-IADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNH
          AR........H..F.TEYVATRWYRAPE.ML....YT..ID.WSVGCI..EML..R..FPGK.Y..QL..
Retrocopy ARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQL

Parental  ILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALA
          I...LG.PS............R.Y.QSLP....V.W....P..D..AL.LL.RML.F.P..RI....AL.
Retrocopy IMMVLGTPSPAVIQAVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALR

Parental  HPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARF
          HP.L..Y.DP.DEP....PF.FA.....L..ER.KE.I..E...F
Retrocopy HPFLAKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDF

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	1.60 RPM	174.55 RPM
SRP007412_cerebellum	1.82 RPM	40.37 RPM
SRP007412_heart	0.63 RPM	9.63 RPM
SRP007412_kidney	3.35 RPM	29.67 RPM
SRP007412_liver	1.25 RPM	13.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1440 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017108	1 retrocopy	retro_cfam_1254,
Dasypus novemcinctus	ENSDNOG00000002191	1 retrocopy	retro_dnov_1241,
Loxodonta africana	ENSLAFG00000017904	1 retrocopy	retro_lafr_1022,
Myotis lucifugus	ENSMLUG00000011284	1 retrocopy	retro_mluc_1697,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pongo abelii	ENSPPYG00000007239	1 retrocopy	retro_pabe_1440 ,
Rattus norvegicus	ENSRNOG00000019601	1 retrocopy	retro_rnor_831,