RetrogeneDB ID: retro_btau_1300

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:104179777..104181543(-)
• Located in intron of: ENSBTAG00000004585

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.92467
• Ensembl ID: ENSBTAG00000034225
• Aliases: None
• Description: None

Sequence

>retro_btau_1300
ATGAAACGGGTCCGCACGGAGCAGATCAGATGGCCGTGTCCTGCTACCTCAAACGCCGGCAGTACGGGGATGCGGACGGC
CCGCTGAAGCAAGGCCTGCGGCTGTCGCAGAGCACTGAGGAGATGGCTGCCAGCCTCACAGTCCAATCAGAATCTGGTTG
TGCCAACATAGTGTCCGCAGCCCCTTGCCAGGCAGAGCCCCAACAATATGAAGTACAGTTCGGACGGCTGTGGAATTTTC
TCACCGATTCTGACTCCCAGCACAGCCATGAAGTGATGCCTCTCCTCTACCCTCTCTTTGTCTACCTCCATCTCACCCTG
ATCCAGAACAGTCCGAAGAGCACAGCGGAAAGCTTTTACAGCCGCTTCCATGGAATGTTTCTGCAGAACGCCAGCCGGAA
GGATGTTATGGAGCAGCTCTAGACCACTCAGATCGTCCAGGACATCCTGTCTAACTTCCGGCTGCGAGCCTTCCTGGACA
ACAAATACGTGGTTCGTCTGCAGGAAGACAGCTACAGCTACCTTCTCCGCTACCTCCAGAGTGACAACAACACCGCGCTG
TGCAGGATCCTCGCCTGGCACATCCATCTGGACGTGCAGCCCGCCAAGAGGATGGACTACCAGCTCTACGCCAGTGGTGG
CTTCTCCCACGGCGAGGGCAGCGGCCTGGAGCCCACCGACATGCCAGCGCCCATCCTGCAGAATAAGGCCGCCCTGGAGC
TCCTGCAGAAGAGCATCAAGCGTGTCAAGGACAGCCCCCCCTCCCTCACCACCATCTACTTCTACGCCTTCTACAACACG
GAGCAGCTGCTGAACACTGCAGAGGTCTCCCCGAACAGCAAGCTGCTCGCAGCAGGCTTTGACAACTCCTGTATAAAACT
GTGGAGTCTGTGTTCCGAGAAGTTAAAGTCCAAACCCCATCAAGTAGATGTGTCCCGCATCCACTTGGCTTGTGATTTCC
TAGAGGAGGAGGATGACGAGGATGACAACGCAGGCACAGAGATGAAGGTCCTGCGGGGACACTGCGGGCCAGTGTACAGC
ACCAGGTTCCTCGCGGACAGCTCGGGGCTGCTCTCCTGCTCTGAAGACATGTCCATCAGGTACTGGGACCTGGGCAGCTT
CACCAACACCGTGCTGTACCAGGGCCACGCCTACCCCGTGTGGGACCTGGACATCAGCCCGCACAGCCTGTACTTCGCCA
GCGGGTCGCACGACCGCACAGCCCGGCTGTGGTCATTTGATCGGACGTACCCACTGCGAATCTTCGCCGGGCACCTGGCA
GACGTGGACTGCGTCAAGTTCCACCCCAATTCAAACTACTTAGCCACGGGCTCAACCGACAAGACGGTGCGGCTGTGGAG
CACTCAGCAGGGGAACTCAGTGAGGCTCTTCACGGGCCACCGCGGCCCTGTGCTCTCCCTGGCTTTTTCCCCCAACAGTA
AGTACCTGGCATCAGCAGGCGAGGACCAGCGGCTGAAGCTATGGGACTTGGCGTCTGGGACCCTCTACAAAGAGCTGCGG
GGCCACACGGACAGCATCACCAGCCTCACCTTCAGCTCAGACAGCAGCCTGATCGCATCAGCGTCCATGGACAACTCTGT
GCGTGTCTGGGACATCAGAAGCACACACTGTAGCACACCCGCCGACGGCTCATCTAGCGAGCTCCTGGGCGTCTATACCA
GCCAGATAAGCAAAGTGCTGAGCGTGCAGTTCATGGCCTGCAACCTCCTGCTGGTGACTGGAATCCCACAAGAAAATCAG
GAACAT

Alignment

ORF - retro_btau_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKRVRTEQI-QMAVSCYLKRRQYGDADGP-KQILRLSQSTEEMAASLTVQSESGCANIVSAAPCQAEPQQ
          MKRVRTEQI.QMAVSCYLKRRQYGDADGP.KQ.LRLSQSTEEMAASLTVQSESGCANIVSAAPCQAEPQQ
Retrocopy MKRVRTEQI<QMAVSCYLKRRQYGDADGPLKQGLRLSQSTEEMAASLTVQSESGCANIVSAAPCQAEPQQ

Parental  YEVQFGRLRNFLTDSDSQHSHEVMPLLYPLFVYLHLTLIQNSPKSTVESFYSRFHGMFLQNASQKDVIEQ
          YEVQFGRL.NFLTDSDSQHSHEVMPLLYPLFVYLHLTLIQNSPKST.ESFYSRFHGMFLQNAS.KDV.EQ
Retrocopy YEVQFGRLWNFLTDSDSQHSHEVMPLLYPLFVYLHLTLIQNSPKSTAESFYSRFHGMFLQNASRKDVMEQ

Parental  LQTTQTIQDILSNFRLRAFLDNKYVVRLQEDSYNYLLRYLQSDNNTALCRILAWHIHLDVQPAKRTDYQL
          L.TTQ..QDILSNFRLRAFLDNKYVVRLQEDSY.YLLRYLQSDNNTALCRILAWHIHLDVQPAKR.DYQL
Retrocopy L*TTQIVQDILSNFRLRAFLDNKYVVRLQEDSYSYLLRYLQSDNNTALCRILAWHIHLDVQPAKRMDYQL

Parental  YTSGGSFRGEGGGLEPADMPAPILQNEAALE---ESIKRVKDGPPSLTTIYFYAFYNTEQLLNTAEVSPD
          Y.SGG...GEG.GLEP.DMPAPILQN.AALE....SIKRVKD.PPSLTTIYFYAFYNTEQLLNTAEVSP.
Retrocopy YASGGFSHGEGSGLEPTDMPAPILQNKAALELLQKSIKRVKDSPPSLTTIYFYAFYNTEQLLNTAEVSPN

Parental  SKLLAAGFDNSCIKLWSLRSKKLKSEPHQVDVSRIHLACDFLEEEDDEDDNLGTEMKVLRGHCGPVYSTR
          SKLLAAGFDNSCIKLWSL.S.KLKS.PHQVDVSRIHLACDFLEEEDDEDDN.GTEMKVLRGHCGPVYSTR
Retrocopy SKLLAAGFDNSCIKLWSLCSEKLKSKPHQVDVSRIHLACDFLEEEDDEDDNAGTEMKVLRGHCGPVYSTR

Parental  FLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPHSLYFASASHDRTARLWSFDRTYPL
          FLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPHSLYFAS.SHDRTARLWSFDRTYPL
Retrocopy FLADSSGLLSCSEDMSIRYWDLGSFTNTVLYQGHAYPVWDLDISPHSLYFASGSHDRTARLWSFDRTYPL

Parental  RIYAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSTQQGNSVRLFTGHRGPVLSLAFSPNGKYLASAGED
          RI.AGHLADVDCVKFHPNSNYLATGSTDKTVRLWSTQQGNSVRLFTGHRGPVLSLAFSPN.KYLASAGED
Retrocopy RIFAGHLADVDCVKFHPNSNYLATGSTDKTVRLWSTQQGNSVRLFTGHRGPVLSLAFSPNSKYLASAGED

Parental  QRLKLWDLASGTLYKELRGHTDNITSLTFSPDSSLVASASMDNSVRVWDIRSSHCSTPADGSSSELVGVY
          QRLKLWDLASGTLYKELRGHTD.ITSLTFS.DSSL.ASASMDNSVRVWDIRS.HCSTPADGSSSEL.GVY
Retrocopy QRLKLWDLASGTLYKELRGHTDSITSLTFSSDSSLIASASMDNSVRVWDIRSTHCSTPADGSSSELLGVY

Parental  TGQMSNVLSVQFMACNLLLVTGITQENQEH
          T.Q.S.VLSVQFMACNLLLVTGI.QENQEH
Retrocopy TSQISKVLSVQFMACNLLLVTGIPQENQEH

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	0.22 RPM	4.11 RPM
ERP005899_muscle	0.84 RPM	11.56 RPM
SRP017611_brain	1.00 RPM	12.65 RPM
SRP017611_kidney	0.71 RPM	12.80 RPM
SRP017611_liver	0.15 RPM	12.76 RPM
SRP030211_testis	3.53 RPM	33.20 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1300 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1300 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015944	1 retrocopy	retro_btau_702,
Bos taurus	ENSBTAG00000034225	1 retrocopy	retro_btau_1300 ,
Callithrix jacchus	ENSCJAG00000010986	1 retrocopy	retro_cjac_4042,
Homo sapiens	ENSG00000135801	1 retrocopy	retro_hsap_1750,
Gorilla gorilla	ENSGGOG00000028544	1 retrocopy	retro_ggor_2253,
Pan troglodytes	ENSPTRG00000002091	1 retrocopy	retro_ptro_1216,
Rattus norvegicus	ENSRNOG00000018027	1 retrocopy	retro_rnor_509,