RetrogeneDB ID: retro_hsap_2369

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:202275269..202276920(-)
• Located in intron of: ENSG00000082146

Retrocopy information

• Ensembl ID: ENSG00000213090
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SCYL2
• Ensembl ID: ENSG00000136021
• Aliases: SCYL2, CVAK104
• Description: SCY1-like 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:19286]

Sequence

>retro_hsap_2369
TTGACTTCAGAATTTGTAAACCCTGACATGGTACCTTTTGTTTTGCCCAGTGTTCTACTGATCGTTGAGGAATGCACCAA
AGAAGAATATGTCACATTAATTCCACCTGAACTTGGCCCTGTGTTTAAGCAGCAGGAGCCAATCCAGATTTTGTTAATTT
TCCTACAAAAAATGGATTTGCTACTAACCAAAACCCCTCCCAATGAGATAAAGAACAGTGTTCTACCCATGGTTTACAGA
GCACTAGAAGCTCCTTCCATTCAATACCAGGAGCTCTGTCTAAACATCATTCCAACCTTTGCAAATCTTATAGACTACCC
ATCATGAAACATACTTTGATACCAAGAATTAAAAATGCCTGTCTACAAATGTCTTCCCTTGCTGTTCCTGTAAATTCATT
AGTGTGCTTAGGAAAGATTTTGGAATACTTGGATAAGTGGTTGGTACTTGATGGTATCCTACCCTTCTTACAACAAATTC
CATCCAAAGAGTCTGCAGTCCTCATGGGTATTTTAGGCATTTACAAATGTACTTTTACTCATAAGTTGGGAATCACCAAA
GAGCAGCTGACTGGAAAAGTATTGCCTCATCTTATTCCCCTGAGTATTGAAAACAATCTTAATCAGTTCAATTCTTTCAT
TTCCATCATAAAAGAGATGCTGAATAGGTTGGAGTCTGAACATAAGACTAAGCTGGAGCAACTTCATATAATGCAAGAAC
AACAGAAATCTTTGGACATAGGAAATCAAATGAATGTTTCTGAGGAGACAAAAGTTACAAATATTGGGAATCAGCAAATT
GACAAGGTTTTTAGCCACATTGGAGCAGACCTTCTGACTGGCAGTGATTCCGAAAATAAAGAGGATGGGTTTCAGAATAA
ACATAAAAGAGCATCACTTACACTTGAAGAAAAACAAAAATTAGCAAGAGAACAAGAGCAGGCATAGAAGTTGAAAGGCC
AGCAGCCTCTTAAACCCCAAGTGTACACACCTATTGCTGCTGTTAAACAGACTAAGGACTTGACAGACACATTGATGGAT
AATATGTCATCTTTGACTAGCCTTTCTGTTAGTACCCCTAAACCTTCTGCTTCAAGTACGTTCACTTCTGTTCCTTCCAT
GGGCATTGACATGATGTTTTCTACACCAGTTGATAATACAAAGAGAAATTTGACAAATGGCCTAAATGTCAATATGGGCT
TTCAGACTTCAGGATTCAACATGCCCGTTACTACAAACCAGAACTTCTACAGTAGTCCAAGCACAGTTGGAGTGACCAAA
ATGACTCTGGAACACCTCCCACTTTGCCAAACTTCAGTGCTTTGAATGTTCCTCCTGCTGGTGCGAAGCCAACCCAACAA
AGACCCACAGATATGTCTGCCCTTAATAATCTCTTTGGCCCTCAGAAACCCAAAGTTAGCATGAACCAATTATCACAACA
GAAACCAAATCAGTGGCTTAATCAGTTTGTACCTCCTCAAGTTTCTCCAGCTACGGGCAGTTCAGTAATGGGAACACAGA
TGAACATGATAGGACAATCTGCCTTTGGTATGCAGGGTAATCCTTTCTTCAACCCACAGAACTTTGCATAGCCACCAACT
GCTATGACCAATAGCAGTTCAGCTAGCAATGATTTTAAAGATCTTTTTGGG

Alignment

ORF - retro_hsap_2369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.73 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTSEFVNPDMVPFVLPNVLLIAEECTKEEYVKLILPELGPVFKQQEPIQILLIFLQKMDLLLTKTPPDEI
          LTSEFVNPDMVPFVLP.VLLI.EECTKEEYV.LI.PELGPVFKQQEPIQILLIFLQKMDLLLTKTPP.EI
Retrocopy LTSEFVNPDMVPFVLPSVLLIVEECTKEEYVTLIPPELGPVFKQQEPIQILLIFLQKMDLLLTKTPPNEI

Parental  KNSVLPMVYRALEAPSIQIQELCLNIIPTFANLIDYPS-MKNALIPRIKNACLQTSSLAVRVNSLVCLGK
          KNSVLPMVYRALEAPSIQ.QELCLNIIPTFANLIDYPS.MK..LIPRIKNACLQ.SSLAV.VNSLVCLGK
Retrocopy KNSVLPMVYRALEAPSIQYQELCLNIIPTFANLIDYPS<MKHTLIPRIKNACLQMSSLAVPVNSLVCLGK

Parental  ILEYLDKWFVLDDILPFLQQIPSKEPAVLMGILGIYKCTFTHKKLGITKEQLAGKVLPHLIPLSIENNLN
          ILEYLDKW.VLD.ILPFLQQIPSKE.AVLMGILGIYKCTFTHK.LGITKEQL.GKVLPHLIPLSIENNLN
Retrocopy ILEYLDKWLVLDGILPFLQQIPSKESAVLMGILGIYKCTFTHK-LGITKEQLTGKVLPHLIPLSIENNLN

Parental  LNQFNSFISVIKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGNQMNVSEEMKVTNIGNQQIDKVFNNIGA
          ..QFNSFIS.IKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGNQMNVSEE.KVTNIGNQQIDKVF..IGA
Retrocopy --QFNSFISIIKEMLNRLESEHKTKLEQLHIMQEQQKSLDIGNQMNVSEETKVTNIGNQQIDKVFSHIGA

Parental  DLLTGSESENKEDGLQNKHKRASLTLEEKQKLAKEQEQAQKLKSQQPLKPQVHTPVATVKQTKDLTDTLM
          DLLTGS.SENKEDG.QNKHKRASLTLEEKQKLA.EQEQA.KLK.QQPLKPQV.TP.A.VKQTKDLTDTLM
Retrocopy DLLTGSDSENKEDGFQNKHKRASLTLEEKQKLAREQEQA*KLKGQQPLKPQVYTPIAAVKQTKDLTDTLM

Parental  DNMSSLTSLSVSTPKSSASSTFTSVPSMGIGMMFSTPTDNTKRNLTNGLNANMGFQTSGFNMPVNTNQNF
          DNMSSLTSLSVSTPK.SASSTFTSVPSMGI.MMFSTP.DNTKRNLTNGLN.NMGFQTSGFNMPV.TNQNF
Retrocopy DNMSSLTSLSVSTPKPSASSTFTSVPSMGIDMMFSTPVDNTKRNLTNGLNVNMGFQTSGFNMPVTTNQNF

Parental  YSSPSTVGVTKMTL-GTPPTLPNFNALSVPPAGAKQTQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQ
          YSSPSTVGVTKMTL.GTPPTLPNF.AL.VPPAGAK.TQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQ
Retrocopy YSSPSTVGVTKMTL<GTPPTLPNFSALNVPPAGAKPTQQRPTDMSALNNLFGPQKPKVSMNQLSQQKPNQ

Parental  WLNQFVPPQGSPTMGSSVMGTQMNVIGQSAFGMQGNPFFNPQNFAQPPTTMTNSSSASNDLKDLFG
          WLNQFVPPQ.SP..GSSVMGTQMN.IGQSAFGMQGNPFFNPQNFA.PPT.MTNSSSASND.KDLFG
Retrocopy WLNQFVPPQVSPATGSSVMGTQMNMIGQSAFGMQGNPFFNPQNFA*PPTAMTNSSSASNDFKDLFG

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
bodymap2_adipose	0.58 RPM	53.15 RPM
bodymap2_adrenal	0.68 RPM	49.92 RPM
bodymap2_brain	0.42 RPM	42.40 RPM
bodymap2_breast	0.41 RPM	62.59 RPM
bodymap2_colon	0.00 RPM	70.40 RPM
bodymap2_heart	0.24 RPM	53.57 RPM
bodymap2_kidney	0.12 RPM	102.06 RPM
bodymap2_liver	0.04 RPM	54.10 RPM
bodymap2_lung	0.09 RPM	74.70 RPM
bodymap2_lymph_node	0.00 RPM	60.14 RPM
bodymap2_ovary	0.19 RPM	84.01 RPM
bodymap2_prostate	0.07 RPM	77.84 RPM
bodymap2_skeletal_muscle	0.02 RPM	45.16 RPM
bodymap2_testis	0.11 RPM	71.53 RPM
bodymap2_thyroid	0.17 RPM	75.08 RPM
bodymap2_white_blood_cells	0.06 RPM	102.55 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2369 was not detected

EST

No EST(s) were mapped for retro_hsap_2369 retrocopy.

TSS

No TSS is located nearby retro_hsap_2369 retrocopy 5' end.

Lab

retro_hsap_2369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2369 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000136021	1 retrocopy	retro_hsap_2369 ,
Gorilla gorilla	ENSGGOG00000002948	1 retrocopy	retro_ggor_1799,
Macaca mulatta	ENSMMUG00000023600	1 retrocopy	retro_mmul_957,
Pongo abelii	ENSPPYG00000004865	1 retrocopy	retro_pabe_2139,
Sarcophilus harrisii	ENSSHAG00000011140	1 retrocopy	retro_shar_569,