RetrogeneDB ID: retro_btau_676

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:38326308..38327234(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000016059
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NFYA
• Ensembl ID: ENSBTAG00000009905
• Aliases: NFYA, CBF-B, NF-YA
• Description: Nuclear transcription factor Y subunit alpha [Source:UniProtKB/Swiss-Prot;Acc:Q5E9S2]

Sequence

>retro_btau_676
ATGAAACACTATACAGCCAACAGCAATAGTTCAACAGAGCAGACTATTGTACAGGCTGGACAGACTCAGCAGCAGGTCCA
AGGGCAGCCACTATTGGTACAGGTCAGTGGAGGCTGGTTAGTCACATCAACTGGCCAACTATCATGGTCCAAGCTCTTCC
TGGTAGACAAGGTCAAACCTTTATGCAGGTACCTGTGTCTGGGACACGGGGTTTGCAGCAGATACAGTTGGTCCCACCAG
GACAGATCCAGATCCAGGGTGGGCAGGCTGTGCAAGTGCAGTGCCAGACCCAGCAGATCATCATCCAGCAGCCCCAGACG
GCCATCATTGCTGGCCAGACACAGACACAGCAGCAGATTGCTCTCCAGGGGCAGCAAGTGGCACAGACTGCTGAAAGGCA
GACCATTGTCTATCAGCCAGTTAATGCAGATGGCACCATTCTACAGCAAGGCATGATCACCATCCCCACAGCCAGTCTGG
CAGGAGCACAGACTGTTCTTATGGAAGGTGACACCAACACAACTAGCAGTGGGCAAGGGACTGTCATTGTGACATTTCCA
GTGGCAGGCAATGTGGTTAATTCAGGAGGGATGGTCATGATGGTACCTGGTGCTGGCTCTGTGCCTACAATTCAGAGAAT
CCCTCTCCCTGGGCTGAAGATGCTTGAAGAAGAGCCTCTCTACATCAGTGCCAAACAGTATCACCTTATATTTAAGAGGA
GGCAAGCTCGGACTAAATTAGAGGCAGAAGGGAAAATTCCGAAGGAAAGAAGGAAATACTTGCATGAGTCTCAACACCAT
CATGCCATGGTATGGAAGTGTGATGAAGGCAGACGATTTTTCTCTCCAAAGGAAAAAGATAGTCCCCATATGCAGGATCC
AAGTCAAGCAGATGAAGGGGCTGTGACCCAGATCATCCAAGTGTCC

Alignment

ORF - retro_btau_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEQYAANSNSSAEQIVVQAGQIQQQVQGQPLMVQVSGGQLITSTGQ-PIMVQAVPGGQGQTIMQVPVSGT
          M..Y.ANSNSS.EQ..VQAGQ.QQQVQGQPL.VQVSGG.L.TSTGQ..IMVQA.PG.QGQT.MQVPVSGT
Retrocopy MKHYTANSNSSTEQTIVQAGQTQQQVQGQPLLVQVSGGWLVTSTGQ<TIMVQALPGRQGQTFMQVPVSGT

Parental  QGLQQIQLVPPGQIQIQGGQAVQVQGQQGQTQQIIIQQPQTAVTAGQTQTQQQIAVQGQQVAQTAEGQTI
          .GLQQIQLVPPGQIQIQGGQAVQV...Q.QTQQIIIQQPQTA..AGQTQTQQQIA.QGQQVAQTAE.QTI
Retrocopy RGLQQIQLVPPGQIQIQGGQAVQV---QCQTQQIIIQQPQTAIIAGQTQTQQQIALQGQQVAQTAERQTI

Parental  VYQPVNADGTILQQGMITIPAASLAGAQIVQTGANTNTTSSGQGTVTVTLPVAGNVVNSGGMVMMVPGAG
          VYQPVNADGTILQQGMITIP.ASLAGAQ.V.....TNTTSSGQGTV.VT.PVAGNVVNSGGMVMMVPGAG
Retrocopy VYQPVNADGTILQQGMITIPTASLAGAQTVLMEGDTNTTSSGQGTVIVTFPVAGNVVNSGGMVMMVPGAG

Parental  SVPAIQRIPLPGAEMLEEEPLYVNAKQYHRILKRRQARAKLEAEGKIPKERRKYLHESRHRHAMARKRGE
          SVP.IQRIPLPG..MLEEEPLY..AKQYH.I.KRRQAR.KLEAEGKIPKERRKYLHES.H.HAM..K..E
Retrocopy SVPTIQRIPLPGLKMLEEEPLYISAKQYHLIFKRRQARTKLEAEGKIPKERRKYLHESQHHHAMVWKCDE

Parental  GGRFFSPKEKDSPHMQDPNQADEEAMTQIIRVS
          G.RFFSPKEKDSPHMQDP.QADE.A.TQII.VS
Retrocopy GRRFFSPKEKDSPHMQDPSQADEGAVTQIIQVS

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
ERP005899_liver	0.00 RPM	8.00 RPM
ERP005899_muscle	0.00 RPM	14.94 RPM
SRP017611_brain	0.00 RPM	8.45 RPM
SRP017611_kidney	0.00 RPM	12.33 RPM
SRP017611_liver	0.00 RPM	6.19 RPM
SRP030211_testis	0.00 RPM	20.13 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_676 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004435	1 retrocopy	retro_amel_1701,
Bos taurus	ENSBTAG00000009905	1 retrocopy	retro_btau_676 ,
Ictidomys tridecemlineatus	ENSSTOG00000023405	1 retrocopy	retro_itri_1410,