RetrogeneDB ID: retro_ggal_20

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: AADN03015686.1:2311..3076(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK1
• Ensembl ID: ENSGALG00000001501
• Aliases: None
• Description: mitogen-activated protein kinase 1 [Source:RefSeq peptide;Acc:NP_989481]

Sequence

>retro_ggal_20
TACGTGGTGCTGGACCTGATGGAGTCGGACCTCCACCAGATCATCCACTCCTCGCAGCCCCTGACTTTGGAACACGTCCG
CTACTTCCTCTACCAGCTCCTTCGCGGCCTCAAATACATCCATTCGGCCAACGTCCTCCACCGGGACCTCAAACCTTCCA
ACCTTTTGGTCAACGAGAACTGCGAGCTGAAGATCGGCGATTTCGGTATGGCCAGGGGGCTCGGAGCGGACCCCCGCCAT
AGCAAAGCCTTCCTGACCGAATACGTGGCCACACGGTGGTACCGGGCTCCGGAACTGCTCCTATCCTTACACCGTTACAC
CCGAGCCATCGACATGTGGTCGGTGGGTTGCATCTTCGCCGAGATGTTGGGCCGCCGACAGCTCTTCCCGGGTCGCAATT
ACGTCCATCAGCTGCAGCTCATCATGGCCGTCCTGGGGACCCCCCCCGCGGGCGTCATGGCGGCCATCGGGGCCGAGAGG
GTCCGCGCCTACCTGCAGAGCCTCCCCCCTCGCCCCCCGGTGCCGTGGGAGAGCCTTTACGGCGACGCCGAGCCGGCGGC
GTTGGCGCTGTTGGGGAGGATGCTGAGGTTCGACCCCAGGGAGAGGGTGGGGGTGGCCGAAGCGTTGCGCCATCCCTTCC
TGGCCAAATACCACGACCCCGAGGATGAGCCCGAGTGCATCCCGGCCTTCGACTTCGCCTTCGAGCGCCGCGTGCTCACC
AAGGAGGAGATCAAAGCCGCCATCGTGGCCGAGATCGAGGATTTC

Alignment

ORF - retro_ggal_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 79.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YIVQDLMETDLYKLL-KTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGL
          Y.V.DLME.DL.......Q.L...H..YFLYQ.LRGLKYIHSANVLHRDLKPSNLL.N..C.LKI.DFG.
Retrocopy YVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYIHSANVLHRDLKPSNLLVNENCELKIGDFGM

Parental  ARVADPDHDHT-GFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNH
          AR....D..H...FLTEYVATRWYRAPE..L....YT..ID.WSVGCI.AEML..R..FPG..Y..QL..
Retrocopy ARGLGADPRHSKAFLTEYVATRWYRAPELLLSLHRYTRAIDMWSVGCIFAEMLGRRQLFPGRNYVHQLQL

Parental  ILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADPKALDLLDKMLTFNPHKRIEVEQALA
          I...LG.........I.....R.YL.SLP....VPW..L...A.P.AL.LL..ML.F.P..R..V..AL.
Retrocopy IMAVLGXXXAGVMAAIGAERVRAYLQSLPPRPPVPWESLYGDAEPAALALLGRMLRFDPRERVGVAEALR

Parental  HPYLEQYYDPSDEPVAEAPFKFDMELDDLPKEKLKELIFEETARF
          HP.L..Y.DP.DEP.....F.F..E...L.KE..K..I..E...F
Retrocopy HPFLAKYHDPEDEPECIPAFDFAFERRVLTKEEIKAAIVAEIEDF

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	3.59 RPM	138.43 RPM
SRP007412_cerebellum	3.42 RPM	96.91 RPM
SRP007412_heart	1.63 RPM	19.13 RPM
SRP007412_kidney	2.54 RPM	33.03 RPM
SRP007412_liver	1.57 RPM	9.13 RPM
SRP007412_testis	10.41 RPM	20.29 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_20 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_20 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_20 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010312	1 retrocopy	retro_btau_498,
Ficedula albicollis	ENSFALG00000007935	1 retrocopy	retro_falb_19,
Gallus gallus	ENSGALG00000001501	1 retrocopy	retro_ggal_20 ,
Myotis lucifugus	ENSMLUG00000005952	1 retrocopy	retro_mluc_302,
Monodelphis domestica	ENSMODG00000017722	1 retrocopy	retro_mdom_101,
Ochotona princeps	ENSOPRG00000014484	2 retrocopies	retro_opri_242, retro_opri_615,