RetrogeneDB ID: retro_falb_19

Retrocopy location

• Organism: Flycatcher (Ficedula albicollis)
• Coordinates: AGTO01023814.1:3673..4203(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK1
• Ensembl ID: ENSFALG00000007935
• Aliases: None
• Description: mitogen-activated protein kinase 1 [Source:HGNC Symbol;Acc:6871]

Sequence

>retro_falb_19
CCAACGATTGGCCAAACCCAGTCAGCTACGTCGTTCTTGACCTGATGGAGAGCGACCTCCACCAAATCATCCACTCGGCG
CAGCCGCTGACGCTGGAGCACGTCCGCTACTTCCTCTACCAACTCCTCCGCGGCCTCAAGTACATCCACTCGGCCAACGT
CCTCCACCGCGACCTCAAGCCCAGCAACCTGCTGGTCAACGAGAACTGCGAGCTCAAGATCGGCGACTTCGGCATGGCGC
GCGGCCTGGGCGCCGACCCGCGCCAGGCCAAGGCCTTCCTCACCGAGTACGTGGCCACGCGCTGGTACCGCGCGCCGGAG
CTGCTGCTCTCGCTGCACCGCTACACGCGCGCCATCGACATGTGGTCGGTCGGCTGCATCTTCGCCGAGATGCTCGGCCG
CCGGCAGCTCTTCCCCGGCCGCAACTACGTGCACCAGCTGCAGCTGATCATGGCGGTGCTGGGCACGCCGCCGGCCGGCG
TCATGGCGGCCATCGGCGCCGAGCGGGTGCGCGCCTACGTGCAGAGCCTG

Alignment

ORF - retro_falb_19 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.18 %
• Parental protein coverage: 54.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTIEQMKDV-YIVQDLMETDLYKLLKT-QHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTT
          PTI.Q.....Y.V.DLME.DL.......Q.L...H..YFLYQ.LRGLKYIHSANVLHRDLKPSNLL.N..
Retrocopy PTIGQTQSA<YVVLDLMESDLHQIIHSAQPLTLEHVRYFLYQLLRGLKYIHSANVLHRDLKPSNLLVNEN

Parental  CDLKICDFGLARVADPD-HDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFP
          C.LKI.DFG.AR....D......FLTEYVATRWYRAPE..L....YT..ID.WSVGCI.AEML..R..FP
Retrocopy CELKIGDFGMARGLGADPRQAKAFLTEYVATRWYRAPELLLSLHRYTRAIDMWSVGCIFAEMLGRRQLFP

Parental  GKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSL
          G..Y..QL..I...LG.P.......I.....R.Y..SL
Retrocopy GRNYVHQLQLIMAVLGTPPAGVMAAIGAERVRAYVQSL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ficedula albicollis was not studied using RNA-Seq expression data.

ChIP-Seq

Ficedula albicollis was not studied using ChIP-Seq data.

EST

Ficedula albicollis was not studied using EST data.

TSS

Ficedula albicollis was not studied using FANTOM5 data.

Lab

retro_falb_19 was not experimentally validated.

Homology

Retrocopy orthology:

Ficedula albicollis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,